From 7afc44fd0d6323c3501e7c70612d8010e0ecb9fd Mon Sep 17 00:00:00 2001 From: Anne Marie Noronha Date: Mon, 31 Mar 2025 14:44:00 -0400 Subject: [PATCH 1/5] accommodate more outputs --- modules/nf-core/portcullis/full/main.nf | 28 +++- modules/nf-core/portcullis/full/meta.yml | 132 ++++++++++++++++-- .../portcullis/full/tests/main.nf.test | 7 + .../portcullis/full/tests/main.nf.test.snap | 56 +++++++- .../portcullis/full/tests/nextflow.config | 11 ++ 5 files changed, 207 insertions(+), 27 deletions(-) create mode 100644 modules/nf-core/portcullis/full/tests/nextflow.config diff --git a/modules/nf-core/portcullis/full/main.nf b/modules/nf-core/portcullis/full/main.nf index 22628713920b..1c2948244a85 100644 --- a/modules/nf-core/portcullis/full/main.nf +++ b/modules/nf-core/portcullis/full/main.nf @@ -13,10 +13,16 @@ process PORTCULLIS_FULL { tuple val(meta3), path(fasta) output: - tuple val(meta), path("*.log"), emit: log - tuple val(meta), path("*.bed"), emit: bed - tuple val(meta), path("*.tab"), emit: tab - path "versions.yml" , emit: versions + tuple val(meta), path("*.log") , emit: log + tuple val(meta), path("*.pass.junctions.bed"), emit: pass_junctions_bed + tuple val(meta), path("*.bed") , emit: bed + tuple val(meta), path("*.pass.junctions.tab"), emit: pass_junctions_tab + tuple val(meta), path("*.tab") , emit: tab + tuple val(meta), path("*.intron.gff3") , emit: intron_gff , optional: true + tuple val(meta), path("*.exon.gff3") , emit: exon_gff , optional: true + tuple val(meta), path("*.bam") , emit: spliced_bam, optional:true + tuple val(meta), path("*.bai") , emit: spliced_bai, optional:true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -36,6 +42,16 @@ process PORTCULLIS_FULL { cp ${prefix}/3-filt/*.bed . cp ${prefix}/3-filt/*.tab . + if [ -f ${prefix}/3-filt/*.pass.junctions.intron.gff3 ] ; then + cp ${prefix}/3-filt/*.pass.junctions.intron.gff3 . + fi + if [ -f ${prefix}/3-filt/*.pass.junctions.exon.gff3 ] ; then + cp ${prefix}/3-filt/*.pass.junctions.exon.gff3 . + fi + if [ -f ${prefix}/2-junc/*.spliced.bam ] ; then + cp ${prefix}/2-junc/*.spliced.bam . + cp ${prefix}/2-junc/*.spliced.bam.bai . + fi cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -48,8 +64,8 @@ process PORTCULLIS_FULL { def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.portcullis.log - touch ${prefix}.portcullis.bed - touch ${prefix}.portcullis.tab + touch ${prefix}.pass.junctions.bed + touch ${prefix}.pass.junctions.tab cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/portcullis/full/meta.yml b/modules/nf-core/portcullis/full/meta.yml index d67743c81744..402cc8e67fa4 100644 --- a/modules/nf-core/portcullis/full/meta.yml +++ b/modules/nf-core/portcullis/full/meta.yml @@ -9,8 +9,8 @@ tools: - "portcullis": description: "Portcullis is a tool that filters out invalid splice junctions from RNA-seq alignment data. It accepts BAM files from various RNA-seq mappers, analyzes - splice junctions and removes likely false positives, outputting filtered - results in multiple formats for downstream analysis." + splice junctions and removes likely false positives, outputting filtered results + in multiple formats for downstream analysis." homepage: "https://portcullis.readthedocs.io/en/latest/index.html" documentation: "https://portcullis.readthedocs.io/en/latest/using.html" doi: "10.1101/217620" @@ -60,13 +60,31 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] pattern: "*.log" + ontologies: &id001 + - edam: "http://edamontology.org/format_2330" - "*.log": - type: file - description: Log file containing Portcullis execution details, processing steps, - and filtering statistics + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*.log" - ontologies: - - edam: "http://edamontology.org/format_2330" + ontologies: *id001 + - pass_junctions_bed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.pass.junctions.bed" + ontologies: &id002 + - edam: "http://edamontology.org/format_3003" + - "*.pass.junctions.bed": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.pass.junctions.bed" + ontologies: *id002 - bed: - meta: type: map @@ -74,13 +92,31 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] pattern: "*.bed" + ontologies: &id003 + - edam: "http://edamontology.org/format_3003" - "*.bed": - type: file + type: map description: | - Filtered splice junction coordinates in BED format, containing genomic coordinates of valid splice junctions after filtering out false positives + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*.bed" - ontologies: - - edam: "http://edamontology.org/format_3003" + ontologies: *id003 + - pass_junctions_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.pass.junctions.tab" + ontologies: &id004 + - edam: "http://edamontology.org/format_3475" + - "*.pass.junctions.tab": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.pass.junctions.tab" + ontologies: *id004 - tab: - meta: type: map @@ -88,13 +124,80 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] pattern: "*.tab" + ontologies: &id005 + - edam: "http://edamontology.org/format_3475" - "*.tab": type: map description: | - Tabular representation of filtered splice junctions with additional metrics including junction scores, read support, and filtering decision data + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*.tab" - ontologies: - - eadam: "http://edamontology.org/format_3475" + ontologies: *id005 + - intron_gff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.intron.gff3" + ontologies: &id006 + - edam: "http://edamontology.org/format_1975" + - "*.intron.gff3": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.intron.gff3" + ontologies: *id006 + - exon_gff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.exon.gff3" + ontologies: &id007 + - edam: "http://edamontology.org/format_1975" + - "*.exon.gff3": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.exon.gff3" + ontologies: *id007 + - spliced_bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.bam" + ontologies: &id008 + - edam: "http://edamontology.org/format_2572" + - "*.bam": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.bam" + ontologies: *id008 + - spliced_bai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.bai" + ontologies: &id009 + - edam: "http://edamontology.org/format_3327" + + - "*.bai": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.bai" + ontologies: *id009 - versions: - versions.yml: type: file @@ -106,3 +209,4 @@ authors: - "@jblancoheredia" maintainer: - "@jblancoheredia" + - "@anoronh4" diff --git a/modules/nf-core/portcullis/full/tests/main.nf.test b/modules/nf-core/portcullis/full/tests/main.nf.test index fe7e9ff06dc1..d7f50b0468cc 100644 --- a/modules/nf-core/portcullis/full/tests/main.nf.test +++ b/modules/nf-core/portcullis/full/tests/main.nf.test @@ -10,6 +10,7 @@ nextflow_process { tag "portcullis/full" test("portcullis_full_paired_end") { + config "./nextflow.config" when { process { @@ -36,6 +37,8 @@ nextflow_process { { assert snapshot( process.out.bed, process.out.tab, + process.out.intron_gff, + process.out.exon_gff, process.out.versions ).match() } @@ -70,8 +73,12 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( + process.out.pass_junctions_bed, process.out.bed, + process.out.pass_junctions_tab, process.out.tab, + process.out.intron_gff, + process.out.exon_gff, process.out.versions ).match() } diff --git a/modules/nf-core/portcullis/full/tests/main.nf.test.snap b/modules/nf-core/portcullis/full/tests/main.nf.test.snap index 995bed3e85f8..266ccbcd1e87 100644 --- a/modules/nf-core/portcullis/full/tests/main.nf.test.snap +++ b/modules/nf-core/portcullis/full/tests/main.nf.test.snap @@ -27,15 +27,33 @@ ] ] ], + [ + [ + { + "id": "test", + "single_end": false + }, + "portcullis_filtered.pass.junctions.intron.gff3:md5,3ee2c3526bfb54f81bfd55a3ab679570" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "portcullis_filtered.pass.junctions.exon.gff3:md5,7a3c56aca8dcd39ee2dec40589511a81" + ] + ], [ "versions.yml:md5,b297b098450e5baaea436e822fe25b0e" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "24.10.3" }, - "timestamp": "2025-03-07T08:45:09.959686" + "timestamp": "2025-03-28T23:14:30.547673" }, "portcullis_full_paired_end_stub": { "content": [ @@ -45,7 +63,25 @@ "id": "test", "single_end": false }, - "test.portcullis.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.pass.junctions.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.pass.junctions.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.pass.junctions.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -54,8 +90,14 @@ "id": "test", "single_end": false }, - "test.portcullis.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.pass.junctions.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + [ + + ], + [ + ], [ "versions.yml:md5,b297b098450e5baaea436e822fe25b0e" @@ -63,8 +105,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "24.10.3" }, - "timestamp": "2025-03-07T08:45:14.189846" + "timestamp": "2025-03-28T23:14:38.848916" } -} +} \ No newline at end of file diff --git a/modules/nf-core/portcullis/full/tests/nextflow.config b/modules/nf-core/portcullis/full/tests/nextflow.config new file mode 100644 index 000000000000..671cdd5bcd4b --- /dev/null +++ b/modules/nf-core/portcullis/full/tests/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: PORTCULLIS_FULL { + ext.args = { + [ + "--intron_gff", + "--exon_gff", + "--separate" + ].join(" ").trim() + } + } +} From 3be0a3fb64d175c97df2ceb2fa37bea1fc866897 Mon Sep 17 00:00:00 2001 From: Juan Blanco Heredia <135283452+jblancoheredia@users.noreply.github.com> Date: Mon, 31 Mar 2025 16:09:43 -0400 Subject: [PATCH 2/5] Update main.nf --- modules/nf-core/portcullis/full/main.nf | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/portcullis/full/main.nf b/modules/nf-core/portcullis/full/main.nf index 1c2948244a85..96a05b306c47 100644 --- a/modules/nf-core/portcullis/full/main.nf +++ b/modules/nf-core/portcullis/full/main.nf @@ -13,15 +13,13 @@ process PORTCULLIS_FULL { tuple val(meta3), path(fasta) output: - tuple val(meta), path("*.log") , emit: log tuple val(meta), path("*.pass.junctions.bed"), emit: pass_junctions_bed - tuple val(meta), path("*.bed") , emit: bed tuple val(meta), path("*.pass.junctions.tab"), emit: pass_junctions_tab - tuple val(meta), path("*.tab") , emit: tab + tuple val(meta), path("*.portcullis.log") , emit: log tuple val(meta), path("*.intron.gff3") , emit: intron_gff , optional: true tuple val(meta), path("*.exon.gff3") , emit: exon_gff , optional: true - tuple val(meta), path("*.bam") , emit: spliced_bam, optional:true - tuple val(meta), path("*.bai") , emit: spliced_bai, optional:true + tuple val(meta), path("*.bam") , emit: spliced_bam, optional: true + tuple val(meta), path("*.bai") , emit: spliced_bai, optional: true path "versions.yml" , emit: versions when: @@ -40,8 +38,8 @@ process PORTCULLIS_FULL { $fasta \\ $bam > ${prefix}.portcullis.log - cp ${prefix}/3-filt/*.bed . - cp ${prefix}/3-filt/*.tab . + cp ${prefix}/3-filt/*.pass.junctions.bed . + cp ${prefix}/3-filt/*.pass.junctions.tab . if [ -f ${prefix}/3-filt/*.pass.junctions.intron.gff3 ] ; then cp ${prefix}/3-filt/*.pass.junctions.intron.gff3 . fi @@ -49,8 +47,8 @@ process PORTCULLIS_FULL { cp ${prefix}/3-filt/*.pass.junctions.exon.gff3 . fi if [ -f ${prefix}/2-junc/*.spliced.bam ] ; then - cp ${prefix}/2-junc/*.spliced.bam . cp ${prefix}/2-junc/*.spliced.bam.bai . + cp ${prefix}/2-junc/*.spliced.bam . fi cat <<-END_VERSIONS > versions.yml From 6773656c83cd33eea8da29aaafb629a28c1ebcff Mon Sep 17 00:00:00 2001 From: Juan Blanco Heredia <135283452+jblancoheredia@users.noreply.github.com> Date: Mon, 31 Mar 2025 16:34:08 -0400 Subject: [PATCH 3/5] Update meta.yml --- modules/nf-core/portcullis/full/meta.yml | 124 +++++++---------------- 1 file changed, 35 insertions(+), 89 deletions(-) diff --git a/modules/nf-core/portcullis/full/meta.yml b/modules/nf-core/portcullis/full/meta.yml index 402cc8e67fa4..c6a5f87cb958 100644 --- a/modules/nf-core/portcullis/full/meta.yml +++ b/modules/nf-core/portcullis/full/meta.yml @@ -58,146 +58,92 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'sample1', single_end:false ] + - "*.portcullis.log": + type: file + description: Log file containing Portcullis execution details, processing steps, + and filtering statistics pattern: "*.log" - ontologies: &id001 + ontologies: - edam: "http://edamontology.org/format_2330" - - "*.log": - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.log" - ontologies: *id001 - pass_junctions_bed: - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.pass.junctions.bed" - ontologies: &id002 - - edam: "http://edamontology.org/format_3003" + e.g. [ id:'sample1', single_end:false ] - "*.pass.junctions.bed": - type: map + type: file description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Filtered splice junction coordinates in BED format, containing genomic coordinates of valid splice junctions after filtering out false positives pattern: "*.pass.junctions.bed" - ontologies: *id002 - - bed: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.bed" - ontologies: &id003 + ontologies: - edam: "http://edamontology.org/format_3003" - - "*.bed": - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.bed" - ontologies: *id003 - pass_junctions_tab: - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.pass.junctions.tab" - ontologies: &id004 - - edam: "http://edamontology.org/format_3475" + e.g. [ id:'sample1', single_end:false ] - "*.pass.junctions.tab": - type: map + type: file description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Tabular representation of filtered splice junctions with additional metrics including junction scores, read support, and filtering decision data pattern: "*.pass.junctions.tab" - ontologies: *id004 - - tab: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.tab" - ontologies: &id005 - - edam: "http://edamontology.org/format_3475" - - "*.tab": - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.tab" - ontologies: *id005 + ontologies: + - eadam: "http://edamontology.org/format_3475" - intron_gff: - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.intron.gff3" - ontologies: &id006 - - edam: "http://edamontology.org/format_1975" + e.g. [ id:'sample1', single_end:false ] - "*.intron.gff3": - type: map + type: file description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Output intron-based junctions in GFF format. pattern: "*.intron.gff3" - ontologies: *id006 + ontologies: + - edam: "http://edamontology.org/format_1975" - exon_gff: - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.exon.gff3" - ontologies: &id007 - - edam: "http://edamontology.org/format_1975" + e.g. [ id:'sample1', single_end:false ] - "*.exon.gff3": - type: map + type: file description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Output exon-based junctions in GFF format. pattern: "*.exon.gff3" - ontologies: *id007 + ontologies: + - edam: "http://edamontology.org/format_1975" - spliced_bam: - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.bam" - ontologies: &id008 - - edam: "http://edamontology.org/format_2572" + e.g. [ id:'sample1', single_end:false ] - "*.bam": - type: map + type: file description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + BAM file after filtering original BAM file by removing alignments associated with bad junctions pattern: "*.bam" - ontologies: *id008 + ontologies: + - edam: "http://edamontology.org/format_2572" - spliced_bai: - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "*.bai" - ontologies: &id009 - - edam: "http://edamontology.org/format_3327" - + e.g. [ id:'sample1', single_end:false ] - "*.bai": - type: map + type: file description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Index of the output BAM file pattern: "*.bai" - ontologies: *id009 + ontologies: + - edam: "http://edamontology.org/format_3327" - versions: - versions.yml: type: file From 187d5510d7bac208e2f48d23ee2201d615e6dc08 Mon Sep 17 00:00:00 2001 From: Anne Marie Noronha Date: Mon, 31 Mar 2025 16:50:22 -0400 Subject: [PATCH 4/5] update nf-test assertions and snapshot --- .../portcullis/full/tests/main.nf.test | 8 ++-- .../portcullis/full/tests/main.nf.test.snap | 44 ++++++++----------- 2 files changed, 22 insertions(+), 30 deletions(-) diff --git a/modules/nf-core/portcullis/full/tests/main.nf.test b/modules/nf-core/portcullis/full/tests/main.nf.test index d7f50b0468cc..32437d178d2f 100644 --- a/modules/nf-core/portcullis/full/tests/main.nf.test +++ b/modules/nf-core/portcullis/full/tests/main.nf.test @@ -35,10 +35,12 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.bed, - process.out.tab, + process.out.pass_junctions_bed, + process.out.pass_junctions_tab, process.out.intron_gff, process.out.exon_gff, + process.out.spliced_bam, + process.out.spliced_bai, process.out.versions ).match() } @@ -74,9 +76,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.pass_junctions_bed, - process.out.bed, process.out.pass_junctions_tab, - process.out.tab, process.out.intron_gff, process.out.exon_gff, process.out.versions diff --git a/modules/nf-core/portcullis/full/tests/main.nf.test.snap b/modules/nf-core/portcullis/full/tests/main.nf.test.snap index 266ccbcd1e87..d7c5c7b2800c 100644 --- a/modules/nf-core/portcullis/full/tests/main.nf.test.snap +++ b/modules/nf-core/portcullis/full/tests/main.nf.test.snap @@ -7,10 +7,7 @@ "id": "test", "single_end": false }, - [ - "portcullis_filtered.pass.junctions.bed:md5,613288f6b446359fd0153a7e628e1489", - "portcullis_filtered.rules_in.junctions.bed:md5,572427ab6ea0832a1810ed1e706d3920" - ] + "portcullis_filtered.pass.junctions.bed:md5,613288f6b446359fd0153a7e628e1489" ] ], [ @@ -19,12 +16,7 @@ "id": "test", "single_end": false }, - [ - "portcullis_filtered.pass.junctions.tab:md5,6e2dd7e93f6b7a23d90d3c3c11e99085", - "portcullis_filtered.rules_in.junctions.tab:md5,6e1aaeb5f73b94142cfa9794d7470a6c", - "portcullis_filtered.rules_out.failed.junctions.tab:md5,be919d60ca646342f6edc2f530174353", - "portcullis_filtered.rules_out.passed.junctions.tab:md5,725bc8ad2a2e8e8456123e25cbb5541b" - ] + "portcullis_filtered.pass.junctions.tab:md5,6e2dd7e93f6b7a23d90d3c3c11e99085" ] ], [ @@ -45,25 +37,13 @@ "portcullis_filtered.pass.junctions.exon.gff3:md5,7a3c56aca8dcd39ee2dec40589511a81" ] ], - [ - "versions.yml:md5,b297b098450e5baaea436e822fe25b0e" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" - }, - "timestamp": "2025-03-28T23:14:30.547673" - }, - "portcullis_full_paired_end_stub": { - "content": [ [ [ { "id": "test", "single_end": false }, - "test.pass.junctions.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "portcullis_all.spliced.bam:md5,3357d8e89ba799bce5a8c76f10e247e6" ] ], [ @@ -72,16 +52,28 @@ "id": "test", "single_end": false }, - "test.pass.junctions.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "portcullis_all.spliced.bam.bai:md5,03e4b328e0200d24d49e2316d3d78f4c" ] ], + [ + "versions.yml:md5,b297b098450e5baaea436e822fe25b0e" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-03-31T16:48:18.276728" + }, + "portcullis_full_paired_end_stub": { + "content": [ [ [ { "id": "test", "single_end": false }, - "test.pass.junctions.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.pass.junctions.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -107,6 +99,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-03-28T23:14:38.848916" + "timestamp": "2025-03-31T16:48:26.392204" } } \ No newline at end of file From eb22b0b43ebe3086a8a9e891a95a91d9956c4b65 Mon Sep 17 00:00:00 2001 From: Anne Marie Noronha Date: Tue, 1 Apr 2025 11:09:44 -0400 Subject: [PATCH 5/5] fix bam test --- .../portcullis/full/tests/main.nf.test | 4 ++-- .../portcullis/full/tests/main.nf.test.snap | 22 ++----------------- 2 files changed, 4 insertions(+), 22 deletions(-) diff --git a/modules/nf-core/portcullis/full/tests/main.nf.test b/modules/nf-core/portcullis/full/tests/main.nf.test index 32437d178d2f..e98d3dc99cb5 100644 --- a/modules/nf-core/portcullis/full/tests/main.nf.test +++ b/modules/nf-core/portcullis/full/tests/main.nf.test @@ -34,13 +34,13 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert file(process.out.spliced_bam.get(0).get(1)).name == "portcullis_all.spliced.bam" }, + { assert file(process.out.spliced_bai.get(0).get(1)).name == "portcullis_all.spliced.bam.bai" }, { assert snapshot( process.out.pass_junctions_bed, process.out.pass_junctions_tab, process.out.intron_gff, process.out.exon_gff, - process.out.spliced_bam, - process.out.spliced_bai, process.out.versions ).match() } diff --git a/modules/nf-core/portcullis/full/tests/main.nf.test.snap b/modules/nf-core/portcullis/full/tests/main.nf.test.snap index d7c5c7b2800c..8ee19487bf26 100644 --- a/modules/nf-core/portcullis/full/tests/main.nf.test.snap +++ b/modules/nf-core/portcullis/full/tests/main.nf.test.snap @@ -37,24 +37,6 @@ "portcullis_filtered.pass.junctions.exon.gff3:md5,7a3c56aca8dcd39ee2dec40589511a81" ] ], - [ - [ - { - "id": "test", - "single_end": false - }, - "portcullis_all.spliced.bam:md5,3357d8e89ba799bce5a8c76f10e247e6" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "portcullis_all.spliced.bam.bai:md5,03e4b328e0200d24d49e2316d3d78f4c" - ] - ], [ "versions.yml:md5,b297b098450e5baaea436e822fe25b0e" ] @@ -63,7 +45,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-03-31T16:48:18.276728" + "timestamp": "2025-04-01T11:06:43.691683" }, "portcullis_full_paired_end_stub": { "content": [ @@ -99,6 +81,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-03-31T16:48:26.392204" + "timestamp": "2025-04-01T11:06:52.265624" } } \ No newline at end of file