diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index a77ad8214495..d78be2255563 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -14,7 +14,7 @@ process SAMTOOLS_INDEX { tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.csi") , optional:true, emit: csi tuple val(meta), path("*.crai"), optional:true, emit: crai - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when @@ -27,11 +27,6 @@ process SAMTOOLS_INDEX { -@ ${task.cpus} \\ $args \\ $input - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -40,10 +35,5 @@ process SAMTOOLS_INDEX { "crai" : args.contains("-c") ? "csi" : "bai" """ touch ${input}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 1bed6bca6348..cfa1e026e27b 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -60,13 +60,29 @@ output: description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool + authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index ca34fb5cd417..599a5ac47023 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -67,7 +67,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.csi[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 3836c6bfeb70..e1bfdeded369 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -18,7 +18,11 @@ ], "3": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] ], "bai": [ @@ -35,16 +39,20 @@ "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" + "versions_samtools": [ + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:38.25787" + "timestamp": "2025-12-31T15:25:32.706640639" }, "crai - stub": { "content": [ @@ -65,7 +73,11 @@ ] ], "3": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] ], "bai": [ @@ -82,16 +94,20 @@ "csi": [ ], - "versions": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" + "versions_samtools": [ + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:34.496412" + "timestamp": "2025-12-31T15:25:24.477945713" }, "bai - stub": { "content": [ @@ -112,7 +128,11 @@ ], "3": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] ], "bai": [ [ @@ -129,29 +149,39 @@ "csi": [ ], - "versions": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" + "versions_samtools": [ + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:25.934431" + "timestamp": "2025-12-31T15:25:16.221396835" }, "csi": { "content": [ "test.paired_end.sorted.bam.csi", - [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:22.262088" + "timestamp": "2025-12-31T15:25:08.621945161" }, "crai": { "content": [ @@ -172,7 +202,11 @@ ] ], "3": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] ], "bai": [ @@ -189,16 +223,20 @@ "csi": [ ], - "versions": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" + "versions_samtools": [ + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:18.191664" + "timestamp": "2025-12-31T15:25:01.071934898" }, "bai": { "content": [ @@ -219,7 +257,11 @@ ], "3": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] ], "bai": [ [ @@ -236,15 +278,19 @@ "csi": [ ], - "versions": [ - "versions.yml:md5,b8717818c91b07de87c2a5590bad02e6" + "versions_samtools": [ + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-10T14:13:08.51539" + "timestamp": "2025-12-31T15:24:52.105615274" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/main.nf b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/main.nf index 54c42b986863..8a62cbb54602 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/main.nf +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/main.nf @@ -12,7 +12,7 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE { main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // // umicollapse in bam mode (thus hardcode mode input channel to 'bam') @@ -24,7 +24,7 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE { // Index BAM file and run samtools stats, flagstat and idxstats // SAMTOOLS_INDEX ( UMICOLLAPSE.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + // SAMTOOLS_INDEX emits version as a topic channel ch_bam_bai_dedup = UMICOLLAPSE.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap index a4aad63142ae..dc2612a69f94 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap @@ -21,15 +21,14 @@ [ "versions.yml:md5,15a99b83c8965f9b29d0e9e6dbdef621", "versions.yml:md5,61bd927f2f2121e34d94692a62305955", - "versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7", - "versions.yml:md5,71d8ff70a0f65311659c446278f10b1a" + "versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:35:06.350407" + "timestamp": "2025-12-31T15:30:53.374645362" }, "test_bam_dedup_stats_samtools_umicollapse_flagstats": { "content": [ diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf index fe6ff312f95b..9a763d663849 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf @@ -25,7 +25,7 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS { // Index BAM file and run samtools stats, flagstat and idxstats // SAMTOOLS_INDEX ( UMITOOLS_DEDUP.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + // SAMTOOLS_INDEX emits version as a topic channel ch_bam_bai_dedup = UMITOOLS_DEDUP.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap index 91045746bbee..3523fc54673f 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap @@ -29,15 +29,14 @@ [ "versions.yml:md5,0ebfc47a75bd075329a7434161100f8f", "versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5", - "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45", - "versions.yml:md5,e687e4e909255370121fcbec5a4299d1" + "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:35:42.524116" + "timestamp": "2025-12-31T15:28:36.488926399" }, "sarscov2_bam_bai - stub": { "content": [ @@ -96,8 +95,7 @@ "7": [ "versions.yml:md5,0ebfc47a75bd075329a7434161100f8f", "versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5", - "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45", - "versions.yml:md5,e687e4e909255370121fcbec5a4299d1" + "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45" ], "bai": [ [ @@ -153,15 +151,14 @@ "versions": [ "versions.yml:md5,0ebfc47a75bd075329a7434161100f8f", "versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5", - "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45", - "versions.yml:md5,e687e4e909255370121fcbec5a4299d1" + "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45" ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:35:58.59434" + "timestamp": "2025-12-31T15:28:52.020714406" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_dedup_umi/main.nf b/subworkflows/nf-core/bam_dedup_umi/main.nf index 5f466563d3bc..91336c60fbfd 100644 --- a/subworkflows/nf-core/bam_dedup_umi/main.nf +++ b/subworkflows/nf-core/bam_dedup_umi/main.nf @@ -22,7 +22,7 @@ workflow BAM_DEDUP_UMI { ch_transcript_fasta // channel: [ val(meta), path(fasta) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() if (umi_dedup_tool != "umicollapse" && umi_dedup_tool != "umitools"){ error("Unknown umi_dedup_tool '${umi_dedup_tool}'") @@ -112,7 +112,7 @@ workflow BAM_DEDUP_UMI { .mix(UMI_DEDUP_GENOME.out.flagstat) .mix(UMI_DEDUP_GENOME.out.idxstats) .transpose() - .map{it[1]} + .map{it -> it[1]} // Record versions diff --git a/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test.snap index 45dd1fc595eb..655170efcab4 100644 --- a/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test.snap @@ -27,7 +27,6 @@ ] ], [ - "versions.yml:md5,0807c0719cb97d193fd38e6588f15521", "versions.yml:md5,1a58acadd4b29b9fa08966dc33d30c1f", "versions.yml:md5,7eaf0c81f627dde8e2710a57e19b4d87", "versions.yml:md5,98c3ba7c6b08a4638ab37ee3fef1213c" @@ -35,9 +34,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T14:40:15.086389" + "timestamp": "2026-01-06T15:06:12.252954811" }, "sarscov2_bam_bai - umitools - with transcriptome bams": { "content": [ @@ -86,8 +85,6 @@ ] ], [ - "versions.yml:md5,2b80da6b65aeb7abca04a2d9f1619fbc", - "versions.yml:md5,50f79167a70eef4c0b788f9b206416ba", "versions.yml:md5,5e97f36286ca959f8dac4c43c54d020f", "versions.yml:md5,69d8142e036d91a3b4d1f41320bcf495", "versions.yml:md5,75264687081ce1cddb24c191058a9926", @@ -98,8 +95,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T14:39:15.42054" + "timestamp": "2026-01-06T15:05:55.280807815" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf index 4ea7416cc23b..a399f9df785f 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/main.nf +++ b/subworkflows/nf-core/bam_markduplicates_picard/main.nf @@ -23,8 +23,8 @@ workflow BAM_MARKDUPLICATES_PICARD { ch_markdup = PICARD_MARKDUPLICATES.out.bam.mix(PICARD_MARKDUPLICATES.out.cram) SAMTOOLS_INDEX ( ch_markdup ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - + // SAMTOOLS_INDEX emits version as a topic channel + ch_reads_index = ch_markdup .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) .join(SAMTOOLS_INDEX.out.crai, by: [0], remainder: true) diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap index 5e24e12bc7cb..d3abaf9c7183 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -9,15 +9,14 @@ [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:37:26.3247" + "timestamp": "2025-12-31T15:38:03.533462011" }, "sarscov2 - bam - stub": { "content": [ @@ -88,7 +87,6 @@ "9": [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ], "bai": [ @@ -157,16 +155,15 @@ "versions": [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:37:50.805524" + "timestamp": "2025-12-31T15:38:18.383834349" }, "homo_sapiens - cram - stub": { "content": [ @@ -231,7 +228,6 @@ "9": [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ], "bai": [ @@ -294,16 +290,15 @@ "versions": [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:38:18.069303" + "timestamp": "2025-12-31T15:38:32.66096122" }, "sarscov2 - bam": { "content": [ @@ -315,14 +310,13 @@ [ "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1", "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f", - "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92", "versions.yml:md5,fb2919b16758582cf470a86acd1f1886" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T02:36:56.78063" + "timestamp": "2025-12-31T15:37:45.881867868" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf index ccef09d88bdf..1ab1c3e0e3da 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf @@ -18,8 +18,8 @@ workflow BAM_SORT_STATS_SAMTOOLS { SAMTOOLS_SORT ( ch_bam, ch_fasta, '' ) SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - + // SAMTOOLS_INDEX emits version as a topic channel + SAMTOOLS_SORT.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index 239f163c79d3..f25eadc0e30d 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -29,16 +29,15 @@ ] ], [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:04:39.140333" + "timestamp": "2025-12-31T15:46:28.41005684" }, "test_bam_sort_stats_samtools_paired_end": { "content": [ @@ -70,16 +69,15 @@ ] ], [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:04:48.787289" + "timestamp": "2025-12-31T15:46:41.207890143" }, "test_bam_sort_stats_samtools_single_end - stub": { "content": [ @@ -133,7 +131,6 @@ ] ], "6": [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ], @@ -186,7 +183,6 @@ ] ], "versions": [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] @@ -194,9 +190,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:05:00.693649" + "timestamp": "2025-12-31T15:46:53.869513128" }, "test_bam_sort_stats_samtools_paired_end - stub": { "content": [ @@ -250,7 +246,6 @@ ] ], "6": [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ], @@ -303,7 +298,6 @@ ] ], "versions": [ - "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5", "versions.yml:md5,6a93080732801bacb21c3acbe13858a5", "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312" ] @@ -311,8 +305,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:05:10.863912" + "timestamp": "2025-12-31T15:47:06.637070905" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_split_by_region/main.nf b/subworkflows/nf-core/bam_split_by_region/main.nf index 50442c767d5e..d37506fe082a 100644 --- a/subworkflows/nf-core/bam_split_by_region/main.nf +++ b/subworkflows/nf-core/bam_split_by_region/main.nf @@ -52,8 +52,8 @@ workflow BAM_SPLIT_BY_REGION { // SAMTOOLS_INDEX(SAMTOOLS_VIEW.out.bam) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - + // SAMTOOLS_INDEX emits version as a topic channel + // // Emit channel in the same format as was taken in by joining each bam with its bai. // diff --git a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap index 231fbf637caf..2724a3998798 100644 --- a/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_split_by_region/tests/main.nf.test.snap @@ -17,14 +17,14 @@ "test_chr21:25689497-46709983.bam.bai" ], [ - "versions.yml:md5,dc397c6f4dc6299aa10c99e9dc303ed1" + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-25T15:33:47.930917" + "timestamp": "2025-12-31T15:42:59.721587569" }, "homo_sapiens - test_paired_end_markduplicates_sorted_bam - stub": { "content": [ @@ -59,7 +59,7 @@ ] ], "1": [ - "versions.yml:md5,dc397c6f4dc6299aa10c99e9dc303ed1" + ], "bam_bai": [ [ @@ -91,14 +91,14 @@ ] ], "versions": [ - "versions.yml:md5,dc397c6f4dc6299aa10c99e9dc303ed1" + ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-25T15:31:05.89921" + "timestamp": "2025-12-31T15:43:13.448986463" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_bamcmp_bwa/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_bamcmp_bwa/tests/main.nf.test.snap index ac02a7dbac0c..e7e08bc6c7b9 100644 --- a/subworkflows/nf-core/fastq_align_bamcmp_bwa/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_bamcmp_bwa/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test.bam.bai:md5,b03370e75a759af24fc46da3b34505c5" + "test.bam.bai:md5,acd8c3c196a49d44d81304370995bf83" ] ], [ @@ -44,7 +44,7 @@ { "id": "test" }, - "test.bam.bai:md5,82450c3162e18e90e85d887d72550cf8" + "test.bam.bai:md5,9ce9f9ca423dea9abaacfd705d57bd0f" ] ], [ @@ -78,8 +78,6 @@ "versions.yml:md5,1517fe0078871eb5fc84e0454d3c3dd6", "versions.yml:md5,1e009c9c98d6ef8695147d1c2512cfeb", "versions.yml:md5,6303b8cfc91c8a3959ebc33c9b8f5b17", - "versions.yml:md5,651abc85c3ce748c6468458dfd26cdff", - "versions.yml:md5,6957707ab955f91c07bf882ac126acb1", "versions.yml:md5,75b177b84a3847f3948c9f736f09508f", "versions.yml:md5,d9ad9260e6695aa2488c08fdf95ce195", "versions.yml:md5,e3ae7f8c33cc78a9cfbf6b8782e29e86", @@ -88,8 +86,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-27T11:57:02.960718" + "timestamp": "2026-01-06T11:09:38.401403365" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_bowtie2/main.nf b/subworkflows/nf-core/fastq_align_bowtie2/main.nf index cafaa9bf931b..96a1a06abebd 100644 --- a/subworkflows/nf-core/fastq_align_bowtie2/main.nf +++ b/subworkflows/nf-core/fastq_align_bowtie2/main.nf @@ -15,7 +15,7 @@ workflow FASTQ_ALIGN_BOWTIE2 { main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // // Map reads with Bowtie2 diff --git a/subworkflows/nf-core/fastq_align_bowtie2/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_bowtie2/tests/main.nf.test.snap index 581a92e060ca..23ab3c3a86f9 100644 --- a/subworkflows/nf-core/fastq_align_bowtie2/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_bowtie2/tests/main.nf.test.snap @@ -49,15 +49,14 @@ [ "versions.yml:md5,4805a7e43a0f0f7ac7708a111a77061e", "versions.yml:md5,b65ab93ae154ffb969c5cfc02b468076", - "versions.yml:md5,fa2e93a14d4a24dbddd775ce552017c7", - "versions.yml:md5,ffde6154951071f3ceb4ccca9f8c0425" + "versions.yml:md5,fa2e93a14d4a24dbddd775ce552017c7" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:52:34.156454" + "timestamp": "2026-01-06T11:10:27.697440767" }, "test_align_bowtie2_single_end": { "content": [ @@ -109,15 +108,14 @@ [ "versions.yml:md5,4805a7e43a0f0f7ac7708a111a77061e", "versions.yml:md5,b65ab93ae154ffb969c5cfc02b468076", - "versions.yml:md5,fa2e93a14d4a24dbddd775ce552017c7", - "versions.yml:md5,ffde6154951071f3ceb4ccca9f8c0425" + "versions.yml:md5,fa2e93a14d4a24dbddd775ce552017c7" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:51:44.612799" + "timestamp": "2026-01-06T11:09:54.818512544" }, "test_align_bowtie2_paired_end": { "content": [ @@ -169,15 +167,14 @@ [ "versions.yml:md5,4805a7e43a0f0f7ac7708a111a77061e", "versions.yml:md5,b65ab93ae154ffb969c5cfc02b468076", - "versions.yml:md5,fa2e93a14d4a24dbddd775ce552017c7", - "versions.yml:md5,ffde6154951071f3ceb4ccca9f8c0425" + "versions.yml:md5,fa2e93a14d4a24dbddd775ce552017c7" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:52:10.824235" + "timestamp": "2026-01-06T11:10:11.165205714" }, "test_align_bowtie2_paired_end - stub": { "content": [ @@ -229,14 +226,13 @@ [ "versions.yml:md5,4805a7e43a0f0f7ac7708a111a77061e", "versions.yml:md5,b65ab93ae154ffb969c5cfc02b468076", - "versions.yml:md5,fa2e93a14d4a24dbddd775ce552017c7", - "versions.yml:md5,ffde6154951071f3ceb4ccca9f8c0425" + "versions.yml:md5,fa2e93a14d4a24dbddd775ce552017c7" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:52:57.091552" + "timestamp": "2026-01-06T11:10:43.375972924" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_bwa/main.nf b/subworkflows/nf-core/fastq_align_bwa/main.nf index c7408d085fff..7050b2b12ef8 100644 --- a/subworkflows/nf-core/fastq_align_bwa/main.nf +++ b/subworkflows/nf-core/fastq_align_bwa/main.nf @@ -13,7 +13,7 @@ workflow FASTQ_ALIGN_BWA { ch_fasta // channel (optional) : [ val(meta3), path(fasta) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // // Map reads with BWA diff --git a/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test b/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test index 7262325a1b69..7a99f233fc9f 100644 --- a/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test @@ -37,9 +37,17 @@ nextflow_workflow { } then { + assert workflow.success assertAll( - { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert snapshot( + bam(workflow.out.bam_orig.get(0).get(1)).getReadsMD5(), + bam(workflow.out.bam.get(0).get(1)).getReadsMD5(), + file(workflow.out.bai.get(0).get(1)).name, + workflow.out.stats, + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.versions.collect{ path(it).yaml } + ).match() } ) } } @@ -68,9 +76,17 @@ nextflow_workflow { } then { + assert workflow.success assertAll( - { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert snapshot( + bam(workflow.out.bam_orig.get(0).get(1)).getReadsMD5(), + bam(workflow.out.bam.get(0).get(1)).getReadsMD5(), + file(workflow.out.bai.get(0).get(1)).name, + workflow.out.stats, + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.versions.collect{ path(it).yaml } + ).match() } ) } } diff --git a/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap index 26866be142f5..788445fd0bef 100644 --- a/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap @@ -1,276 +1,116 @@ { "fastq_align_bwa_paired_end": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,5dbdcfdba65fac634dcbb6984cffe2c4" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,ba4b90f87517a16a6ae6142f37a75d79" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.bai:md5,4c5e6fa0e71327b79034eebd652f2121" - ] - ], - "3": [ - - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.stats:md5,75934f2a51780a80d2ab4674301a018d" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.flagstat:md5,18d602435a02a4d721b78d1812622159" - ] - ], - "6": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.idxstats:md5,85d20a901eef23ca50c323638a2eb602" - ] - ], - "7": [ - "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", - "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", - "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", - "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.bai:md5,4c5e6fa0e71327b79034eebd652f2121" - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,ba4b90f87517a16a6ae6142f37a75d79" - ] - ], - "bam_orig": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,5dbdcfdba65fac634dcbb6984cffe2c4" - ] - ], - "csi": [ - - ], - "flagstat": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.flagstat:md5,18d602435a02a4d721b78d1812622159" - ] - ], - "idxstats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.idxstats:md5,85d20a901eef23ca50c323638a2eb602" - ] - ], - "stats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.stats:md5,75934f2a51780a80d2ab4674301a018d" - ] - ], - "versions": [ - "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", - "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", - "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", - "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" + "57aeef88ed701a8ebc8e2f0a381b2a6", + "af8628d9df18b2d3d4f6fd47ef2bb872", + "test.sorted.bam.bai", + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.stats:md5,75934f2a51780a80d2ab4674301a018d" ] - } + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.flagstat:md5,18d602435a02a4d721b78d1812622159" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.idxstats:md5,85d20a901eef23ca50c323638a2eb602" + ] + ], + [ + { + "FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT": { + "samtools": "1.22.1" + } + }, + { + "FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS": { + "samtools": "1.22.1" + } + }, + { + "FASTQ_ALIGN_BWA:BWA_MEM": { + "bwa": "0.7.19-r1273", + "samtools": "1.22.1" + } + } + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:43:05.771242" + "timestamp": "2026-01-06T12:32:18.995614765" }, "fastq_align_bwa_single_end": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,f7af092ddd5203f647ba96b926392c3e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,c406a43adde2d9673e71d8a8c7db7cfd" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam.bai:md5,f79a40341ecfaae11d8621b138d4c2ea" - ] - ], - "3": [ - - ], - "4": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam.stats:md5,0883b19c92a783883b3e11d5bfcc5d6a" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam.flagstat:md5,2191911d72575a2358b08b1df64ccb53" - ] - ], - "6": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam.idxstats:md5,613e048487662c694aa4a2f73ca96a20" - ] - ], - "7": [ - "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", - "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", - "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", - "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" - ], - "bai": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam.bai:md5,f79a40341ecfaae11d8621b138d4c2ea" - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,c406a43adde2d9673e71d8a8c7db7cfd" - ] - ], - "bam_orig": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,f7af092ddd5203f647ba96b926392c3e" - ] - ], - "csi": [ - - ], - "flagstat": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam.flagstat:md5,2191911d72575a2358b08b1df64ccb53" - ] - ], - "idxstats": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam.idxstats:md5,613e048487662c694aa4a2f73ca96a20" - ] - ], - "stats": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam.stats:md5,0883b19c92a783883b3e11d5bfcc5d6a" - ] - ], - "versions": [ - "versions.yml:md5,21c3a69aa768887de1715ea1b442b0ba", - "versions.yml:md5,42e5cc142537f96b0d91f10af4fa6a51", - "versions.yml:md5,819701fe5d2921de66bcb188a5c3cf9b", - "versions.yml:md5,e0f61a88407ffce16662ced57e5f38c9" + "798439cbd7fd81cbcc5078022dc5479d", + "94fcf617f5b994584c4e8d4044e16b4f", + "test.sorted.bam.bai", + [ + [ + { + "id": "test", + "single_end": true + }, + "test.sorted.bam.stats:md5,0883b19c92a783883b3e11d5bfcc5d6a" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.sorted.bam.flagstat:md5,2191911d72575a2358b08b1df64ccb53" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.sorted.bam.idxstats:md5,613e048487662c694aa4a2f73ca96a20" ] - } + ], + [ + { + "FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT": { + "samtools": "1.22.1" + } + }, + { + "FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS": { + "samtools": "1.22.1" + } + }, + { + "FASTQ_ALIGN_BWA:BWA_MEM": { + "bwa": "0.7.19-r1273", + "samtools": "1.22.1" + } + } + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:42:37.663363" + "timestamp": "2026-01-06T12:32:02.891010818" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_bwaaln/main.nf b/subworkflows/nf-core/fastq_align_bwaaln/main.nf index 2e42da0ac7d7..53af0fcc5e24 100644 --- a/subworkflows/nf-core/fastq_align_bwaaln/main.nf +++ b/subworkflows/nf-core/fastq_align_bwaaln/main.nf @@ -10,12 +10,12 @@ include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/mai workflow FASTQ_ALIGN_BWAALN { take: - ch_reads // channel (mandatory): [ val(meta), path(reads) ]. subworkImportant: meta REQUIRES single_end` entry! + ch_reads // channel (mandatory): [ val(meta), path(reads) ] Important: meta REQUIRES single_end` entry! ch_index // channel (mandatory): [ val(meta), path(index) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // WARNING: You must specify in your prefix `meta.id_index` in your `modules.conf` // to ensure that you do not overwrite multiple BAM files from one sample mapped @@ -93,8 +93,8 @@ workflow FASTQ_ALIGN_BWAALN { // Index all SAMTOOLS_INDEX ( ch_bam_for_index ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - + // SAMTOOLS_INDEX emits version as a topic channel + // Remove superfluous internal maps to minimise clutter as much as possible ch_bam_for_emit = ch_bam_for_index.map{ meta, bam -> [meta - meta.subMap('key_read_ref'), bam] } ch_bai_for_emit = SAMTOOLS_INDEX.out.bai.map{ meta, bai -> [meta - meta.subMap('key_read_ref'), bai] } diff --git a/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test b/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test index b61e3b47f6bb..fd5700d7ad81 100644 --- a/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test @@ -45,9 +45,13 @@ nextflow_workflow { } } then { + assert workflow.success assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + bam(workflow.out.bam.get(0).get(1)).getReadsMD5(), + file(workflow.out.bai.get(0).get(1)).name, + workflow.out.versions.collect{ path(it).yaml } + ).match() } ) } } @@ -81,9 +85,13 @@ nextflow_workflow { } } then { + assert workflow.success assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + bam(workflow.out.bam.get(0).get(1)).getReadsMD5(), + file(workflow.out.bai.get(0).get(1)).name, + workflow.out.versions.collect{ path(it).yaml } + ).match() } ) } } @@ -127,9 +135,13 @@ nextflow_workflow { } } then { + assert workflow.success assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + bam(workflow.out.bam.get(0).get(1)).getReadsMD5(), + file(workflow.out.bai.get(0).get(1)).name, + workflow.out.versions.collect{ path(it).yaml } + ).match() } ) } } @@ -178,9 +190,13 @@ nextflow_workflow { } } then { + assert workflow.success assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + bam(workflow.out.bam.get(0).get(1)).getReadsMD5(), + file(workflow.out.bai.get(0).get(1)).name, + workflow.out.versions.collect{ path(it).yaml } + ).match() } ) } } @@ -230,12 +246,13 @@ nextflow_workflow { } } then { + assert workflow.success assertAll( - { assert workflow.success }, { assert snapshot( - workflow.out, + bam(workflow.out.bam.get(0).get(1)).getReadsMD5(), + file(workflow.out.bai.get(0).get(1)).name, workflow.out.versions.collect{ path(it).yaml } - ).match() } + ).match() } ) } } diff --git a/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test.snap index a0dc982e875a..eedecf51c349 100644 --- a/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_bwaaln/tests/main.nf.test.snap @@ -1,562 +1,116 @@ { "test_fastq_align_bwaaln_singleend": { "content": [ - { - "0": [ - 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"id_index": "test" - }, - "test2_test.bam.bai:md5,4f6fcba7e102fdd7682bb50f46966b9c" - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": false, - "id_index": "test" - }, - "test_test.bam:md5,5bc8b37a3711c1eb96d25b922ca1c109" - ], - [ - { - "id": "test2", - "single_end": true, - "id_index": "test" - }, - "test2_test.bam:md5,a7ce25f23ff96708d2c70fd89982be32" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,4763cea7ddd797a715f8205450e5fa94", - "versions.yml:md5,5577d316e15b75e82f53c7c79d400f02", - "versions.yml:md5,af9c0c64caccee923a3960753239c01a", - "versions.yml:md5,f94390f43c6110591280c10e43440f8c" - ] - } + "ae4005223c9eb0f2b11bcd984e088f9c", + "test_test.bam.bai", + [ + { + "FASTQ_ALIGN_BWAALN:BWA_SAMSE": { + "bwa": "0.7.19-r1273", + "samtools": "1.22.1" + } + }, + { + "FASTQ_ALIGN_BWAALN:BWA_ALN": { + "bwa": "0.7.19-r1273" + } + }, + { + "FASTQ_ALIGN_BWAALN:BWA_SAMPE": { + "bwa": "0.7.19-r1273", + "samtools": "1.22.1" + } + } + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:02:18.6899955" + "timestamp": "2026-01-06T15:04:29.076161972" }, "test_fastq_align_bwa_multiref -- stub": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false, - "id_index": "reftest2" - }, - "test_reftest2.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test", - "single_end": false, - "id_index": "reftest" - }, - "test_reftest.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test2", - "single_end": true, - "id_index": "reftest2" - }, - "test2_reftest2.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test2", - "single_end": true, - "id_index": "reftest" - }, - "test2_reftest.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false, - "id_index": "reftest2" - }, - "test_reftest2.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test", - "single_end": false, - "id_index": "reftest" - }, - "test_reftest.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test2", - "single_end": true, - "id_index": "reftest2" - }, - "test2_reftest2.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test2", - "single_end": true, - "id_index": "reftest" - }, - "test2_reftest.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,4763cea7ddd797a715f8205450e5fa94", - "versions.yml:md5,5577d316e15b75e82f53c7c79d400f02", - "versions.yml:md5,af9c0c64caccee923a3960753239c01a", - "versions.yml:md5,f94390f43c6110591280c10e43440f8c" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false, - "id_index": "reftest2" - }, - "test_reftest2.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test", - "single_end": false, - "id_index": "reftest" - }, - "test_reftest.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test2", - "single_end": true, - "id_index": "reftest2" - }, - "test2_reftest2.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test2", - "single_end": true, - "id_index": "reftest" - }, - "test2_reftest.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": false, - "id_index": "reftest2" - }, - "test_reftest2.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test", - "single_end": false, - "id_index": "reftest" - }, - "test_reftest.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test2", - "single_end": true, - "id_index": "reftest2" - }, - "test2_reftest2.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "test2", - "single_end": true, - "id_index": "reftest" - }, - "test2_reftest.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,4763cea7ddd797a715f8205450e5fa94", - "versions.yml:md5,5577d316e15b75e82f53c7c79d400f02", - "versions.yml:md5,af9c0c64caccee923a3960753239c01a", - "versions.yml:md5,f94390f43c6110591280c10e43440f8c" - ] - }, + "d41d8cd98f00b204e9800998ecf8427e", + "test_reftest2.bam.bai", [ { "FASTQ_ALIGN_BWAALN:BWA_SAMSE": { @@ -574,18 +128,13 @@ "bwa": "0.7.19-r1273", "samtools": "1.22.1" } - }, - { - "FASTQ_ALIGN_BWAALN:SAMTOOLS_INDEX": { - "samtools": "1.22.1" - } } ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T11:02:42.97921838" + "timestamp": "2026-01-06T15:05:09.555454392" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_chromap/main.nf b/subworkflows/nf-core/fastq_align_chromap/main.nf index 26b6a4be6218..99800724e85b 100644 --- a/subworkflows/nf-core/fastq_align_chromap/main.nf +++ b/subworkflows/nf-core/fastq_align_chromap/main.nf @@ -16,7 +16,7 @@ workflow FASTQ_ALIGN_CHROMAP { ch_pairs_chr_order // channel (optional): [ pairs_chr_order ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // // Map reads with CHROMAP diff --git a/subworkflows/nf-core/fastq_align_chromap/tests/main.nf.test b/subworkflows/nf-core/fastq_align_chromap/tests/main.nf.test index 25001bcf2add..225961e534f7 100644 --- a/subworkflows/nf-core/fastq_align_chromap/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_chromap/tests/main.nf.test @@ -49,9 +49,16 @@ nextflow_workflow { } } then { + assert workflow.success assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + bam(workflow.out.bam.get(0).get(1)).getReadsMD5(), + file(workflow.out.bai.get(0).get(1)).name, + workflow.out.stats, + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.versions.collect{ path(it).yaml } + ).match() } ) } } @@ -79,9 +86,16 @@ nextflow_workflow { } } then { + assert workflow.success assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + bam(workflow.out.bam.get(0).get(1)).getReadsMD5(), + file(workflow.out.bai.get(0).get(1)).name, + workflow.out.stats, + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.versions.collect{ path(it).yaml } + ).match() } ) } } diff --git a/subworkflows/nf-core/fastq_align_chromap/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_chromap/tests/main.nf.test.snap index 37716d7297f2..9015e4fc70ff 100644 --- a/subworkflows/nf-core/fastq_align_chromap/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_chromap/tests/main.nf.test.snap @@ -1,229 +1,115 @@ { "test_fastq_align_chromap_single_end": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,74b5083e3c8ac8f918986fe0b36a9317" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam.bai:md5,9fcb4c0bf711694916e282e163fba868" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": true - }, - "test.stats:md5,de59e4f73eee31c4fbe8ec3859c5e0e8" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": true - }, - "test.flagstat:md5,99698bba57b57c7ab68b32bc368a0cc5" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": true - }, - "test.idxstats:md5,0ca8c5edb633a2f4c72fb3160cc25abf" - ] - ], - "5": [ - "versions.yml:md5,510f8807b7572d3ba4db55439fc53106", - "versions.yml:md5,a584d136a6740f2f94b8b8da35c9ff8d", - "versions.yml:md5,db9f1b460f62366ec58912561ceb8d99", - "versions.yml:md5,eedbebb60fcac0618ece9ea0b39baa61" - ], - "bai": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam.bai:md5,9fcb4c0bf711694916e282e163fba868" - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": true - }, - "test.sorted.bam:md5,74b5083e3c8ac8f918986fe0b36a9317" - ] - ], - "flagstat": [ - [ - { - "id": "test", - "single_end": true - }, - "test.flagstat:md5,99698bba57b57c7ab68b32bc368a0cc5" - ] - ], - "idxstats": [ - [ - { - "id": "test", - "single_end": true - }, - "test.idxstats:md5,0ca8c5edb633a2f4c72fb3160cc25abf" - ] - ], - "stats": [ - [ - { - "id": "test", - "single_end": true - }, - "test.stats:md5,de59e4f73eee31c4fbe8ec3859c5e0e8" - ] - ], - "versions": [ - "versions.yml:md5,510f8807b7572d3ba4db55439fc53106", - "versions.yml:md5,a584d136a6740f2f94b8b8da35c9ff8d", - "versions.yml:md5,db9f1b460f62366ec58912561ceb8d99", - "versions.yml:md5,eedbebb60fcac0618ece9ea0b39baa61" + "c0753fc123f2bce542a2e425b397c478", + "test.sorted.bam.bai", + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,de59e4f73eee31c4fbe8ec3859c5e0e8" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,99698bba57b57c7ab68b32bc368a0cc5" ] - } + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,0ca8c5edb633a2f4c72fb3160cc25abf" + ] + ], + [ + { + "FASTQ_ALIGN_CHROMAP:CHROMAP_CHROMAP": { + "chromap": "0.2.6-r490", + "samtools": 1.2 + } + }, + { + "FASTQ_ALIGN_CHROMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT": { + "samtools": "1.22.1" + } + }, + { + "FASTQ_ALIGN_CHROMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS": { + "samtools": "1.22.1" + } + } + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:44:01.924722" + "timestamp": "2026-01-06T12:58:10.624148189" }, "test_fastq_align_chromap_paired_end": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,bd04f77fe97bc452dffaef24bf255829" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.bai:md5,8084ffd06103a6d2cd66c4749d301b5c" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,0900a093aaa649986631997b2b4e919d" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,2fa0d90162a1b655863796c2a6bd8f45" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,1adb27b52d4d64b826f48b59d61dcd4d" - ] - ], - "5": [ - "versions.yml:md5,510f8807b7572d3ba4db55439fc53106", - "versions.yml:md5,a584d136a6740f2f94b8b8da35c9ff8d", - "versions.yml:md5,db9f1b460f62366ec58912561ceb8d99", - "versions.yml:md5,eedbebb60fcac0618ece9ea0b39baa61" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.bai:md5,8084ffd06103a6d2cd66c4749d301b5c" - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,bd04f77fe97bc452dffaef24bf255829" - ] - ], - "flagstat": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,2fa0d90162a1b655863796c2a6bd8f45" - ] - ], - "idxstats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,1adb27b52d4d64b826f48b59d61dcd4d" - ] - ], - "stats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,0900a093aaa649986631997b2b4e919d" - ] - ], - "versions": [ - "versions.yml:md5,510f8807b7572d3ba4db55439fc53106", - "versions.yml:md5,a584d136a6740f2f94b8b8da35c9ff8d", - "versions.yml:md5,db9f1b460f62366ec58912561ceb8d99", - "versions.yml:md5,eedbebb60fcac0618ece9ea0b39baa61" + "2f566fc5e68f63e9b4e81da24c8e6ce2", + "test.sorted.bam.bai", + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,0900a093aaa649986631997b2b4e919d" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,2fa0d90162a1b655863796c2a6bd8f45" ] - } + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,1adb27b52d4d64b826f48b59d61dcd4d" + ] + ], + [ + { + "FASTQ_ALIGN_CHROMAP:CHROMAP_CHROMAP": { + "chromap": "0.2.6-r490", + "samtools": 1.2 + } + }, + { + "FASTQ_ALIGN_CHROMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT": { + "samtools": "1.22.1" + } + }, + { + "FASTQ_ALIGN_CHROMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS": { + "samtools": "1.22.1" + } + } + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:44:25.612984" + "timestamp": "2026-01-06T12:58:28.186557408" }, "test_fastq_align_chromap_paired_end -- stub": { "content": [ @@ -276,7 +162,6 @@ "5": [ "versions.yml:md5,510f8807b7572d3ba4db55439fc53106", "versions.yml:md5,a584d136a6740f2f94b8b8da35c9ff8d", - "versions.yml:md5,db9f1b460f62366ec58912561ceb8d99", "versions.yml:md5,eedbebb60fcac0618ece9ea0b39baa61" ], "bai": [ @@ -327,7 +212,6 @@ "versions": [ "versions.yml:md5,510f8807b7572d3ba4db55439fc53106", "versions.yml:md5,a584d136a6740f2f94b8b8da35c9ff8d", - "versions.yml:md5,db9f1b460f62366ec58912561ceb8d99", "versions.yml:md5,eedbebb60fcac0618ece9ea0b39baa61" ] }, @@ -343,11 +227,6 @@ "samtools": "1.22.1" } }, - { - "FASTQ_ALIGN_CHROMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX": { - "samtools": "1.22.1" - } - }, { "FASTQ_ALIGN_CHROMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS": { "samtools": "1.22.1" @@ -357,8 +236,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T13:44:52.52521" + "timestamp": "2026-01-06T11:13:31.115616615" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf index c08686cb542f..f0739b4d1b0a 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf @@ -70,7 +70,7 @@ workflow FASTQ_ALIGN_DEDUP_BISMARK { SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) + // SAMTOOLS_INDEX emits version as a topic channel /* * Run bismark_methylation_extractor diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap index 3067314eeae6..8865a336bfc2 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap @@ -32,12 +32,12 @@ "single_end": false }, [ - "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,275586e525fa8026af3945b6fd372807", - "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,d15db39c712f65679cce464da6152f72", - "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,c860eff2055ebfa5ab51eaa74c844b1a", - "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,e216e668a80eb0af621ea28bf30649a4", - "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,ceed6d29a4364cf820ff8c5e583b207a", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,9c964be8061710e61f9bda2209f725ed" + "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,30c68663531efea0593fe68276cf356e", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,e37e2de703b23e9ccba000810bb7ab58", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,f66dad685ff77e5fbfec182968b13f6e", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,5e74b72e25cbd286744f84b6c5df4647", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,08f3166117614bfff3c8197026cb2154", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.deduplicated.txt.gz:md5,bbac169dcfd041e032ff4b6ec870ee7b" ] ] ], @@ -85,15 +85,14 @@ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", "versions.yml:md5,5271ecfdf6675b6cca97d42d3d49dbba", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", - 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"CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,ceed6d29a4364cf820ff8c5e583b207a", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,9c964be8061710e61f9bda2209f725ed" + "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,a678e95e342c8cef8a797975f08d5d68", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,4f133df5c443632d59d7acc8982faf2f" ] ] ], @@ -589,15 +584,14 @@ [ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", - "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-03T12:54:41.001127" + "timestamp": "2026-01-06T11:18:03.913889355" }, "Params: bismark paired-end | skip_deduplication": { "content": [ @@ -632,12 +626,12 @@ "single_end": false }, [ - "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,a5315ec249edb9e90d04c8cd79574eb6", - "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,d15db39c712f65679cce464da6152f72", - "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,db9ef72b9f85ac7d0a0b70798b6b05a5", + "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,18a770f64b64c44497670f55b21c4c75", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,549a33c739cf6f2c7ac200a96603ff21", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,5257c752b2132f1df04618d6a8458891", "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,e216e668a80eb0af621ea28bf30649a4", - "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,eab3936aeadb93309dc853b911446969", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,9c964be8061710e61f9bda2209f725ed" + "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,1302cdb173671f26f6bfb5652c356446", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,c8d784b5d3f937a7a65bfc9b2beb3f9c" ] ] ], @@ -683,20 +677,19 @@ [ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", - "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-03T12:52:19.185514" + "timestamp": "2026-01-06T11:15:27.912568049" }, "Params: bismark_hisat single-end | default": { "content": [ [ - "dae445da532c973dc9149f3ceba2d2c5" + "8de7f5f8c997820cbe836eba0da1d24e" ], [ "test.sorted.bam.bai" @@ -716,7 +709,7 @@ "id": "test", "single_end": true }, - "SRR389222_sub1_bismark_hisat2.deduplicated.bedGraph.gz:md5,1f1b14f7be535e6098ece13ea1406bfc" + "SRR389222_sub1_bismark_hisat2.deduplicated.bedGraph.gz:md5,0bf376d55cd46d407386ad93ced13dc0" ] ], [ @@ -726,12 +719,12 @@ "single_end": true }, [ - "CHG_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,2845d98bade52fe2a58af52f1afd9b85", - "CHG_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,38ea97af92edf977fc0a5913946cdf79", - "CHH_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,e9bea3cda06742fda721dc19c9bd4069", - "CHH_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,74cdba62469af46b08e08c85b105f1c0", - "CpG_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,a3bb15f7b5ca52a39f3d21d04aea4273", - "CpG_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,01a9201f89b4972a747f0b7975550d5a" + "CHG_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,22dab3b18563f8df646afb814f1a2b4c", + "CHG_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,caec86e372830358c55c8925ab68599f", + "CHH_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,ba2cd9c009e7f051b461a3ba381e9534", + "CHH_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,9050c702f81d66090ced0d6f1972890d", + "CpG_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,05fbe6e0988586c1d960ec46f8e5244a", + "CpG_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,e5e475cc3988f04548b702c39d06e52c" ] ] ], @@ -741,7 +734,7 @@ "id": "test", "single_end": true }, - "SRR389222_sub1_bismark_hisat2.deduplicated.bismark.cov.gz:md5,ec4a2575b47822ef478b3bda35c70590" + "SRR389222_sub1_bismark_hisat2.deduplicated.bismark.cov.gz:md5,d78a7b9bcefb8d1071a518858c9dd0df" ] ], [ @@ -750,7 +743,7 @@ "id": "test", "single_end": true }, - "SRR389222_sub1_bismark_hisat2.deduplicated_splitting_report.txt:md5,21dee8a9f5255af775fde65a52ca5a3f" + "SRR389222_sub1_bismark_hisat2.deduplicated_splitting_report.txt:md5,eca082420fd52346f1578c37af05384a" ] ], [ @@ -759,13 +752,13 @@ "id": "test", "single_end": true }, - "SRR389222_sub1_bismark_hisat2.deduplicated.M-bias.txt:md5,82b760a6824f55f6732297374d77a6ec" + "SRR389222_sub1_bismark_hisat2.deduplicated.M-bias.txt:md5,7704e7386c466da4277d7edfca26835a" ] ], [ "SRR389222_sub1_bismark_hisat2_SE_report.html" ], - "bismark_summary_report.txt:md5,762c303acee29bfffef35b3d9e04d153", + "bismark_summary_report.txt:md5,e13eff8b9f1e0f48f16e08b2bc85f510", [ "SRR389222_sub1_bismark_hisat2.deduplicated.M-bias.txt", "SRR389222_sub1_bismark_hisat2.deduplicated_splitting_report.txt", @@ -779,14 +772,13 @@ "versions.yml:md5,21a99a5163c08c245e13583754f661a2", "versions.yml:md5,5271ecfdf6675b6cca97d42d3d49dbba", "versions.yml:md5,66529e6c765c8ed62c20ab50e919910f", - "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018", - "versions.yml:md5,bd07c3a96f6628bfe0db52bbc2839e99" + "versions.yml:md5,91ee9a6c0d8ef8f8fceb8eb64333e018" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T16:08:32.039526" + "timestamp": "2026-01-06T11:16:47.805181709" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf index 83dbfb3bf1e1..2d147c03479b 100755 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf @@ -99,7 +99,7 @@ workflow FASTQ_ALIGN_DEDUP_BWAMEM { ch_alignment = PICARD_MARKDUPLICATES.out.bam ch_alignment_index = SAMTOOLS_INDEX.out.bai ch_picard_metrics = PICARD_MARKDUPLICATES.out.metrics - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + // SAMTOOLS_INDEX emits version as a topic channel } /* diff --git a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap index 46fda1f8ac21..95d6a602cbe6 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bwamem/tests/main.nf.test.snap @@ -46,15 +46,14 @@ [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", - "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-03T18:07:22.444845091" + "timestamp": "2025-12-31T16:01:34.520934037" }, "Params: bwamem paired-end - skip_deduplication": { "content": [ @@ -183,7 +182,6 @@ "7": [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", - "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ], "bai": [ @@ -257,7 +255,6 @@ "versions": [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", - "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ] }, @@ -273,11 +270,6 @@ "samtools": "1.22.1" } }, - { - "FASTQ_ALIGN_DEDUP_BWAMEM:SAMTOOLS_INDEX": { - "samtools": "1.22.1" - } - }, { "FASTQ_ALIGN_DEDUP_BWAMEM:PICARD_ADDORREPLACEREADGROUPS": { "picard": "3.4.0" @@ -287,9 +279,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-03T18:08:01.772454395" + "timestamp": "2025-12-31T16:02:36.823646005" }, "Params: bwamem paired-end - default": { "content": [ @@ -338,14 +330,13 @@ [ "versions.yml:md5,6fa0c192669339220d5c5735739188ac", "versions.yml:md5,8f2ff4c430c4c5f42631534eaf358833", - "versions.yml:md5,c8ad9ea35566f100e41588f4c271b663", "versions.yml:md5,e0c30eb274e33f3086ff9e694aae2161" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-03T18:07:38.589146631" + "timestamp": "2025-12-31T16:01:58.522939012" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf index 2ea49653372c..4b108f636a64 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf @@ -71,7 +71,7 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH { ch_alignment ) ch_alignment_index = SAMTOOLS_INDEX_ALIGNMENTS.out.bai - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGNMENTS.out.versions) + // SAMTOOLS_INDEX emits version as a topic channel /* * Run samtools flagstat @@ -110,7 +110,7 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH { ch_alignment_index = SAMTOOLS_INDEX_DEDUPLICATED.out.bai ch_picard_metrics = PICARD_MARKDUPLICATES.out.metrics ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_DEDUPLICATED.out.versions) + // SAMTOOLS_INDEX emits version as a topic channel } /* diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap index 885df4ab2064..9fae34d3e49e 100644 --- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap @@ -36,16 +36,14 @@ [ "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", "versions.yml:md5,58f62eabbc05b725b68ae05ad2adab85", - "versions.yml:md5,6c757564e855659911e8721c78ef6303", - "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f", - "versions.yml:md5,f3b8471451c0aab08b19ca4f19d09b7c" + "versions.yml:md5,6c757564e855659911e8721c78ef6303" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:09:53.217361" + "timestamp": "2025-12-31T16:03:03.126765791" }, "Params: bwameth paired-end | skip_deduplication": { "content": [ @@ -82,15 +80,14 @@ ], [ "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", - "versions.yml:md5,6c757564e855659911e8721c78ef6303", - "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f" + "versions.yml:md5,6c757564e855659911e8721c78ef6303" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-03T12:40:33.660146" + "timestamp": "2025-12-31T16:03:40.587580483" }, "Params: bwameth paired-end | default": { "content": [ @@ -129,15 +126,13 @@ [ "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e", "versions.yml:md5,58f62eabbc05b725b68ae05ad2adab85", - "versions.yml:md5,6c757564e855659911e8721c78ef6303", - "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f", - "versions.yml:md5,f3b8471451c0aab08b19ca4f19d09b7c" + "versions.yml:md5,6c757564e855659911e8721c78ef6303" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-03T12:40:19.798072" + "timestamp": "2025-12-31T16:03:24.180471791" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap index 9e34d924e84a..58671a03466c 100644 --- a/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap @@ -46,7 +46,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,1d8fb5dce75cbfb87955c7ee03c17a5f" + "test.bam:md5,f07ba490699f918eb329e63d45a05216" ] ], "1": [ @@ -64,7 +64,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,1d8fb5dce75cbfb87955c7ee03c17a5f" + "test.bam:md5,f07ba490699f918eb329e63d45a05216" ] ], "bam_index": [ @@ -79,10 +79,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T14:32:08.743821" + "timestamp": "2026-01-06T11:23:24.468372311" }, "test_fastq_align_bwa_mem_SE": { "content": [ @@ -191,7 +191,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,504bcc1ac7f8d8e1e728276a4ce4f4d4" + "test.bam:md5,df969e7e799a733f01d807713cdd8569" ] ], "1": [ @@ -209,7 +209,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,504bcc1ac7f8d8e1e728276a4ce4f4d4" + "test.bam:md5,df969e7e799a733f01d807713cdd8569" ] ], "bam_index": [ @@ -224,10 +224,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T12:03:34.617919741" + "timestamp": "2026-01-06T11:23:07.970027464" }, "test_fastq_align_strobealign_SE": { "content": [ @@ -238,7 +238,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,30a9339ac99b881844cf8514f719f204" + "test.bam:md5,d24feb4a26a4e77df8ef4083d6fb7b6f" ] ], "1": [ @@ -256,7 +256,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,30a9339ac99b881844cf8514f719f204" + "test.bam:md5,d24feb4a26a4e77df8ef4083d6fb7b6f" ] ], "bam_index": [ @@ -271,10 +271,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T14:32:01.424171" + "timestamp": "2026-01-06T11:23:16.504506708" }, "test_fastq_align_snapaligner_SE": { "content": [ @@ -285,7 +285,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,9de00a20df23dc66ddf0d9bba2e486c3" + "test.bam:md5,b620983ca2b7c4bc1a60ab740b04a857" ] ], "1": [ @@ -303,7 +303,7 @@ "id": "test", "single_end": true }, - "test.bam:md5,9de00a20df23dc66ddf0d9bba2e486c3" + "test.bam:md5,b620983ca2b7c4bc1a60ab740b04a857" ] ], "bam_index": [ @@ -318,9 +318,9 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-23T12:03:25.88186957" + "timestamp": "2026-01-06T11:22:57.893016121" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_hisat2/main.nf b/subworkflows/nf-core/fastq_align_hisat2/main.nf index 511fe035ce27..a7c2e62798ae 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/main.nf +++ b/subworkflows/nf-core/fastq_align_hisat2/main.nf @@ -11,7 +11,7 @@ workflow FASTQ_ALIGN_HISAT2 { main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap index 149d7dfbaa08..5b43cd8d6013 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap @@ -48,16 +48,15 @@ ], [ "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21", - "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f", "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29", "versions.yml:md5,ec6468a88403ffc733629109b26e2484" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:11:11.528432" + "timestamp": "2026-01-06T11:23:45.000730329" }, "sarscov2 - bam - single_end - stub": { "content": [ @@ -133,7 +132,6 @@ ], "9": [ "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21", - "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f", "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29", "versions.yml:md5,ec6468a88403ffc733629109b26e2484" ], @@ -208,7 +206,6 @@ ], "versions": [ "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21", - "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f", "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29", "versions.yml:md5,ec6468a88403ffc733629109b26e2484" ] @@ -216,9 +213,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:11:57.586261" + "timestamp": "2026-01-06T11:24:24.710718885" }, "sarscov2 - bam - paired_end": { "content": [ @@ -269,16 +266,15 @@ ], [ "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21", - "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f", "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29", "versions.yml:md5,ec6468a88403ffc733629109b26e2484" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:11:28.95845" + "timestamp": "2026-01-06T11:24:05.589720697" }, "sarscov2 - bam - paired_end - stub": { "content": [ @@ -354,7 +350,6 @@ ], "9": [ "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21", - "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f", "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29", "versions.yml:md5,ec6468a88403ffc733629109b26e2484" ], @@ -429,7 +424,6 @@ ], "versions": [ "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21", - "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f", "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29", "versions.yml:md5,ec6468a88403ffc733629109b26e2484" ] @@ -437,8 +431,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-01T03:12:21.057787" + "timestamp": "2026-01-06T11:24:44.292327038" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_mapad/main.nf b/subworkflows/nf-core/fastq_align_mapad/main.nf index 6c114892f3ef..c39cc028c8f0 100644 --- a/subworkflows/nf-core/fastq_align_mapad/main.nf +++ b/subworkflows/nf-core/fastq_align_mapad/main.nf @@ -22,7 +22,7 @@ workflow FASTQ_ALIGN_MAPAD { main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // WARNING: You must specify in your prefix `meta.id_index` in your `modules.conf` // to ensure that you do not overwrite multiple BAM files from one sample mapped diff --git a/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test b/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test index 3d9d7575ef4d..99e119708f95 100644 --- a/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test @@ -48,19 +48,17 @@ nextflow_workflow { } then { + assert workflow.success assertAll( - { assert workflow.success }, { assert snapshot( - workflow.out.bai, - workflow.out.csi, - workflow.out.stats, - workflow.out.flagstat, - workflow.out.idxstats, - workflow.out.versions, - ).match() - }, - { assert file(workflow.out.bam_unsorted.get(0).get(1)).exists() }, - { assert file(workflow.out.bam.get(0).get(1)).exists() }, + bam(workflow.out.bam_unsorted.get(0).get(1)).getReadsMD5(), + bam(workflow.out.bam.get(0).get(1)).getReadsMD5(), + file(workflow.out.bai.get(0).get(1)).name, + workflow.out.stats, + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.versions.collect{ path(it).yaml } + ).match() } ) } } diff --git a/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test.snap index 8895bd90ad5e..300d3b2b0493 100644 --- a/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_mapad/tests/main.nf.test.snap @@ -1,20 +1,9 @@ { "sarscov2 - bam - single_end": { "content": [ - [ - [ - { - "id": "test", - "single_end": true, - "key_read_ref": "test_genome", - "id_index": "genome" - }, - "test.sorted.bam.bai:md5,a14a162090589149cfa5813dee5a6fd2" - ] - ], - [ - - ], + "c9400322149ce77109e940bff78cbed4", + "4886256830f17154f868a33c47d7cb23", + "test.sorted.bam.bai", [ [ { @@ -49,16 +38,27 @@ ] ], [ - "versions.yml:md5,2ccc5e0c31fc7352109ab3361dc2e5fa", - "versions.yml:md5,5895b8c25147b7d44d2be79cb512d347", - "versions.yml:md5,80071a3b6216b49ca3382bdbac6ad8ad", - "versions.yml:md5,b2ce2b3181bdafd3de613c6251e39988" + { + "FASTQ_ALIGN_MAPAD:MAPAD_MAP": { + "mapad": "0.45.0" + } + }, + { + "FASTQ_ALIGN_MAPAD:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS": { + "samtools": "1.22.1" + } + }, + { + "FASTQ_ALIGN_MAPAD:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT": { + "samtools": "1.22.1" + } + } ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-27T11:54:04.374333" + "timestamp": "2026-01-06T13:00:14.816887565" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_star/main.nf b/subworkflows/nf-core/fastq_align_star/main.nf index 00d553d95a6a..f5416c32ed64 100644 --- a/subworkflows/nf-core/fastq_align_star/main.nf +++ b/subworkflows/nf-core/fastq_align_star/main.nf @@ -17,13 +17,13 @@ workflow FASTQ_ALIGN_STAR { main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // // Map reads with STAR // STAR_ALIGN ( ch_reads, ch_index, ch_gtf, val_star_ignore_sjdbgtf, val_seq_platform, val_seq_center ) - ch_versions = ch_versions.mix(STAR_ALIGN.out.versions.first()) + ch_versions = ch_versions.mix(STAR_ALIGN.out.versions) // // Sort, index BAM file and run samtools stats, flagstat and idxstats diff --git a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap index bbe3059bb50b..df81b8c965cf 100644 --- a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap @@ -54,8 +54,6 @@ [ "versions.yml:md5,167faaf660e4936645b0ad5a9d3bf620", "versions.yml:md5,46a72613cfb790412c2d4c3922f031ea", - "versions.yml:md5,484d39e22399f461f7216de15863b7f6", - "versions.yml:md5,6d04615365467e28edbe029904402f96", "versions.yml:md5,79c45f6683c30e93dc8e1f938185dc4d", "versions.yml:md5,902c1e91ef8c57029ea63f7489a4e741", "versions.yml:md5,b42944e4a0114801de264f0eb659ba2a" @@ -63,9 +61,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-27T16:12:09.131407" + "timestamp": "2026-01-06T11:08:10.351998322" }, "homo_sapiens - fastq - paired_end - with_transcriptome": { "content": [ @@ -142,8 +140,6 @@ [ "versions.yml:md5,167faaf660e4936645b0ad5a9d3bf620", "versions.yml:md5,46a72613cfb790412c2d4c3922f031ea", - "versions.yml:md5,484d39e22399f461f7216de15863b7f6", - "versions.yml:md5,6d04615365467e28edbe029904402f96", "versions.yml:md5,79c45f6683c30e93dc8e1f938185dc4d", "versions.yml:md5,902c1e91ef8c57029ea63f7489a4e741", "versions.yml:md5,b42944e4a0114801de264f0eb659ba2a" @@ -151,9 +147,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-27T16:11:12.668701" + "timestamp": "2026-01-06T11:07:20.59960916" }, "homo_sapiens - fastq - single_end": { "content": [ @@ -201,15 +197,14 @@ [ "versions.yml:md5,167faaf660e4936645b0ad5a9d3bf620", "versions.yml:md5,46a72613cfb790412c2d4c3922f031ea", - "versions.yml:md5,6d04615365467e28edbe029904402f96", "versions.yml:md5,902c1e91ef8c57029ea63f7489a4e741" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-26T14:59:10.53084" + "timestamp": "2026-01-06T11:04:54.812917731" }, "homo_sapiens - fastq - paired_end": { "content": [ @@ -257,14 +252,13 @@ [ "versions.yml:md5,167faaf660e4936645b0ad5a9d3bf620", "versions.yml:md5,46a72613cfb790412c2d4c3922f031ea", - "versions.yml:md5,6d04615365467e28edbe029904402f96", "versions.yml:md5,902c1e91ef8c57029ea63f7489a4e741" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-27T16:10:14.208687" + "timestamp": "2026-01-06T11:05:39.905189309" } } \ No newline at end of file