diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 8a0bb298c..e20f29f49 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -59,7 +59,7 @@ jobs: env: NFT_VER: ${{ env.NFT_VER }} with: - max_shards: 7 + max_shards: 14 - name: debug run: | diff --git a/CHANGELOG.md b/CHANGELOG.md index fa8d95361..1debb7a8e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,7 @@ Special thanks to the following for their contributions to the release: - [PR #1558](https://github.com/nf-core/rnaseq/pull/1558) - Remove patches and bump modules for ARM compat - [PR #1560](https://github.com/nf-core/rnaseq/pull/1560) - General modules update, include updating subworkflows for stats fixes - [PR #1563](https://github.com/nf-core/rnaseq/pull/1563) - Version bumps ahead of 3.19.0 release +- [PR #1565](https://github.com/nf-core/rnaseq/pull/1565) - Improve reproducibility with Conda # 3.18.0 - 2024-12-19 diff --git a/modules.json b/modules.json index 878230091..0eb74cb90 100644 --- a/modules.json +++ b/modules.json @@ -275,17 +275,20 @@ "umitools/dedup": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["bam_dedup_stats_samtools_umitools"] + "installed_by": ["bam_dedup_stats_samtools_umitools", "modules"], + "patch": "modules/nf-core/umitools/dedup/umitools-dedup.diff" }, "umitools/extract": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] + "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore", "modules"], + "patch": "modules/nf-core/umitools/extract/umitools-extract.diff" }, "umitools/prepareforrsem": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["bam_dedup_umi", "modules"] + "installed_by": ["bam_dedup_umi", "modules"], + "patch": "modules/nf-core/umitools/prepareforrsem/umitools-prepareforrsem.diff" }, "untar": { "branch": "master", diff --git a/modules/local/deseq2_qc/environment.yml b/modules/local/deseq2_qc/environment.yml index 1f424690c..052ac035f 100644 --- a/modules/local/deseq2_qc/environment.yml +++ b/modules/local/deseq2_qc/environment.yml @@ -2,12 +2,12 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::r-base - - conda-forge::r-optparse - - conda-forge::r-ggplot2 - - conda-forge::r-rcolorbrewer - - conda-forge::r-pheatmap - - bioconda::bioconductor-deseq2 - - bioconda::bioconductor-biocparallel - - bioconda::bioconductor-tximport - - bioconda::bioconductor-complexheatmap + - conda-forge::r-base=4.0.3 + - conda-forge::r-optparse=1.6.6 + - conda-forge::r-ggplot2=3.3.2 + - conda-forge::r-rcolorbrewer=1.1.2 + - conda-forge::r-pheatmap=1.0.12 + - bioconda::bioconductor-deseq2=1.28.0 + - bioconda::bioconductor-biocparallel=1.22.0 + - bioconda::bioconductor-tximport=1.16.0 + - bioconda::bioconductor-complexheatmap=2.4.2 diff --git a/modules/local/deseq2_qc/tests/main.nf.test b/modules/local/deseq2_qc/tests/main.nf.test index a9d35997d..2f0dd30b8 100644 --- a/modules/local/deseq2_qc/tests/main.nf.test +++ b/modules/local/deseq2_qc/tests/main.nf.test @@ -22,11 +22,8 @@ nextflow_process { { assert snapshot( process.out.dists_multiqc, process.out.dists_txt, - process.out.log, process.out.pca_multiqc, process.out.pca_txt, - process.out.rdata, - process.out.size_factors, process.out.versions ).match() } ) diff --git a/modules/local/deseq2_qc/tests/main.nf.test.snap b/modules/local/deseq2_qc/tests/main.nf.test.snap index 1c6bc7105..7b6d50649 100644 --- a/modules/local/deseq2_qc/tests/main.nf.test.snap +++ b/modules/local/deseq2_qc/tests/main.nf.test.snap @@ -12,13 +12,13 @@ "deseq2.pca.vals.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], "3": [ - + ], "4": [ "deseq2.sample.dists.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], "5": [ - + ], "6": [ "R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -37,7 +37,7 @@ "versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5" ], "dists_multiqc": [ - + ], "dists_txt": [ "deseq2.sample.dists.txt:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -46,7 +46,7 @@ "R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" ], "pca_multiqc": [ - + ], "pca_txt": [ "deseq2.pca.vals.txt:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -81,41 +81,25 @@ "parse count data correctly": { "content": [ [ - + ], [ "deseq2.sample.dists.txt:md5,1616ce40eb58ee75640efed219c6bbec" ], [ - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676" - ], - [ - + ], [ "deseq2.pca.vals.txt:md5,4cda8e32ec39326c1350e77b4b607aad" ], - [ - "deseq2.dds.RData:md5,c7c1872e7566321d0c3f7ca56c463088" - ], - [ - [ - "RAP1_IAA_30M_REP1.txt:md5,ce4ff0b74aeedc3dc12a764c3504c9df", - "RAP1_UNINDUCED_REP1.txt:md5,51c9b23be5e82670aceb14f7e58dd867", - "RAP1_UNINDUCED_REP2.txt:md5,2c56106abcd9d31980f672b6e2862ee8", - "WT_REP1.txt:md5,5e3fe5f7e9b7f300be43649a8b496352", - "WT_REP2.txt:md5,2ce093f2c2e92c1bde1cd3da91ac884c", - "deseq2.size_factors.RData:md5,51c6643a0f8a9edabbff8df0165451f2" - ] - ], [ "versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.2" }, - "timestamp": "2024-06-21T11:21:20.349616" + "timestamp": "2025-06-06T11:39:25.276180757" } -} +} \ No newline at end of file diff --git a/modules/local/gtf2bed/environment.yml b/modules/local/gtf2bed/environment.yml index a5d6e3dff..99d32b942 100644 --- a/modules/local/gtf2bed/environment.yml +++ b/modules/local/gtf2bed/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::perl>=5.26.2 + - conda-forge::perl=5.26.2 diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml index e5721f1e7..3ab4fdce4 100644 --- a/modules/nf-core/umitools/dedup/environment.yml +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -5,3 +5,12 @@ channels: - bioconda dependencies: - bioconda::umi_tools=1.1.5 + - python=3.9.18 + - matplotlib=3.8.2 + - scipy=1.12.0 + - regex=2023.12.25 + - numpy=1.26.4 + - pandas=2.2.0 + - pysam=0.22.0 + - future=0.18.3 + - pybktree=1.1 diff --git a/modules/nf-core/umitools/dedup/umitools-dedup.diff b/modules/nf-core/umitools/dedup/umitools-dedup.diff new file mode 100644 index 000000000..d3204eb1f --- /dev/null +++ b/modules/nf-core/umitools/dedup/umitools-dedup.diff @@ -0,0 +1,24 @@ +Changes in component 'nf-core/umitools/dedup' +Changes in 'umitools/dedup/environment.yml': +--- modules/nf-core/umitools/dedup/environment.yml ++++ modules/nf-core/umitools/dedup/environment.yml +@@ -5,3 +5,12 @@ + - bioconda + dependencies: + - bioconda::umi_tools=1.1.5 ++ - python=3.9.18 ++ - matplotlib=3.8.2 ++ - scipy=1.12.0 ++ - regex=2023.12.25 ++ - numpy=1.26.4 ++ - pandas=2.2.0 ++ - pysam=0.22.0 ++ - future=0.18.3 ++ - pybktree=1.1 + +'modules/nf-core/umitools/dedup/meta.yml' is unchanged +'modules/nf-core/umitools/dedup/main.nf' is unchanged +'modules/nf-core/umitools/dedup/tests/main.nf.test.snap' is unchanged +'modules/nf-core/umitools/dedup/tests/nextflow.config' is unchanged +'modules/nf-core/umitools/dedup/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index e5721f1e7..3ab4fdce4 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -5,3 +5,12 @@ channels: - bioconda dependencies: - bioconda::umi_tools=1.1.5 + - python=3.9.18 + - matplotlib=3.8.2 + - scipy=1.12.0 + - regex=2023.12.25 + - numpy=1.26.4 + - pandas=2.2.0 + - pysam=0.22.0 + - future=0.18.3 + - pybktree=1.1 diff --git a/modules/nf-core/umitools/extract/umitools-extract.diff b/modules/nf-core/umitools/extract/umitools-extract.diff new file mode 100644 index 000000000..a32c9112b --- /dev/null +++ b/modules/nf-core/umitools/extract/umitools-extract.diff @@ -0,0 +1,24 @@ +Changes in component 'nf-core/umitools/extract' +Changes in 'umitools/extract/environment.yml': +--- modules/nf-core/umitools/extract/environment.yml ++++ modules/nf-core/umitools/extract/environment.yml +@@ -5,3 +5,12 @@ + - bioconda + dependencies: + - bioconda::umi_tools=1.1.5 ++ - python=3.9.18 ++ - matplotlib=3.8.2 ++ - scipy=1.12.0 ++ - regex=2023.12.25 ++ - numpy=1.26.4 ++ - pandas=2.2.0 ++ - pysam=0.22.0 ++ - future=0.18.3 ++ - pybktree=1.1 + +'modules/nf-core/umitools/extract/meta.yml' is unchanged +'modules/nf-core/umitools/extract/main.nf' is unchanged +'modules/nf-core/umitools/extract/tests/main.nf.test.snap' is unchanged +'modules/nf-core/umitools/extract/tests/nextflow.config' is unchanged +'modules/nf-core/umitools/extract/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml index e5721f1e7..3ab4fdce4 100644 --- a/modules/nf-core/umitools/prepareforrsem/environment.yml +++ b/modules/nf-core/umitools/prepareforrsem/environment.yml @@ -5,3 +5,12 @@ channels: - bioconda dependencies: - bioconda::umi_tools=1.1.5 + - python=3.9.18 + - matplotlib=3.8.2 + - scipy=1.12.0 + - regex=2023.12.25 + - numpy=1.26.4 + - pandas=2.2.0 + - pysam=0.22.0 + - future=0.18.3 + - pybktree=1.1 diff --git a/modules/nf-core/umitools/prepareforrsem/umitools-prepareforrsem.diff b/modules/nf-core/umitools/prepareforrsem/umitools-prepareforrsem.diff new file mode 100644 index 000000000..88eb12de8 --- /dev/null +++ b/modules/nf-core/umitools/prepareforrsem/umitools-prepareforrsem.diff @@ -0,0 +1,23 @@ +Changes in component 'nf-core/umitools/prepareforrsem' +Changes in 'umitools/prepareforrsem/environment.yml': +--- modules/nf-core/umitools/prepareforrsem/environment.yml ++++ modules/nf-core/umitools/prepareforrsem/environment.yml +@@ -5,3 +5,12 @@ + - bioconda + dependencies: + - bioconda::umi_tools=1.1.5 ++ - python=3.9.18 ++ - matplotlib=3.8.2 ++ - scipy=1.12.0 ++ - regex=2023.12.25 ++ - numpy=1.26.4 ++ - pandas=2.2.0 ++ - pysam=0.22.0 ++ - future=0.18.3 ++ - pybktree=1.1 + +'modules/nf-core/umitools/prepareforrsem/meta.yml' is unchanged +'modules/nf-core/umitools/prepareforrsem/main.nf' is unchanged +'modules/nf-core/umitools/prepareforrsem/tests/main.nf.test.snap' is unchanged +'modules/nf-core/umitools/prepareforrsem/tests/main.nf.test' is unchanged +************************************************************ diff --git a/subworkflows/local/align_star/tests/main.nf.test b/subworkflows/local/align_star/tests/main.nf.test index 35b3236e8..e1e584bea 100644 --- a/subworkflows/local/align_star/tests/main.nf.test +++ b/subworkflows/local/align_star/tests/main.nf.test @@ -63,16 +63,14 @@ nextflow_workflow { { assert snapshot( file(workflow.out.log_final[0][1]).name, file(workflow.out.log_out[0][1]).name, - workflow.out.bai, - workflow.out.bam, - workflow.out.bam_sorted, - workflow.out.bam_transcript, + file(workflow.out.bai[0][1]).name, + bam(workflow.out.bam[0][1]).getReadsMD5(), workflow.out.csi, workflow.out.log_progress, workflow.out.fastq, workflow.out.flagstat, workflow.out.idxstats, - workflow.out.orig_bam, + bam(workflow.out.orig_bam[0][1]).getReadsMD5(), workflow.out.stats, workflow.out.tab, workflow.out.versions).match()} @@ -132,16 +130,14 @@ nextflow_workflow { { assert snapshot( file(workflow.out.log_final[0][1]).name, file(workflow.out.log_out[0][1]).name, - workflow.out.bai, - workflow.out.bam, - workflow.out.bam_sorted, - workflow.out.bam_transcript, + file(workflow.out.bai[0][1]).name, + bam(workflow.out.bam[0][1]).getReadsMD5(), workflow.out.csi, workflow.out.log_progress, workflow.out.fastq, workflow.out.flagstat, workflow.out.idxstats, - workflow.out.orig_bam, + bam(workflow.out.orig_bam[0][1]).getReadsMD5(), workflow.out.stats, workflow.out.tab, workflow.out.versions).match()} diff --git a/subworkflows/local/align_star/tests/main.nf.test.snap b/subworkflows/local/align_star/tests/main.nf.test.snap index 992e9b231..c55ad9f23 100644 --- a/subworkflows/local/align_star/tests/main.nf.test.snap +++ b/subworkflows/local/align_star/tests/main.nf.test.snap @@ -3,36 +3,8 @@ "content": [ "test.Log.final.out", "test.Log.out", - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,4cf31974d82bed533f4b6528dff95b50" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,7137528dd300c4ae0f7e3370a5555c79" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,b6cec9bba6b04b9b92eddbef128bdfbb" - ] - ], - [ - - ], + "test.bam.bai", + "1e02b8e6b4a02ab58bfe4ee795aba815", [ ], @@ -66,15 +38,7 @@ "test.idxstats:md5,107ca94dd426cc44db316f0d402307c5" ] ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,b6cec9bba6b04b9b92eddbef128bdfbb" - ] - ], + "db9a8324b5163b025bcc0c33e848486", [ [ { @@ -103,10 +67,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-21T14:53:32.322441137" + "timestamp": "2025-06-06T17:48:18.740399" }, "star - no igenomes - stub": { "content": [ @@ -248,30 +212,8 @@ "content": [ "test.Log.final.out", "test.Log.out", - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,59e8552f0e50c540d41198496bf34251" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,0d47a5f971c1548eadc1f3c39dab0dbf" - ] - ], - [ - - ], - [ - - ], + "test.bam.bai", + "1e02b8e6b4a02ab58bfe4ee795aba815", [ ], @@ -305,15 +247,7 @@ "test.idxstats:md5,107ca94dd426cc44db316f0d402307c5" ] ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,4e917b4befbbe216fd666d06af0298af" - ] - ], + "db9a8324b5163b025bcc0c33e848486", [ [ { @@ -343,9 +277,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.2" }, - "timestamp": "2024-12-19T09:47:39.98853048" + "timestamp": "2025-06-06T17:36:09.274326" }, "star - with igenomes - stub": { "content": [ diff --git a/tests/.nftignore b/tests/.nftignore index 1b79fab54..77b5531ee 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -87,6 +87,7 @@ umitools/*.umi_extract.log {multiqc,multiqc/**}/multiqc_report_data/umitools_stats_violin.txt {multiqc,multiqc/**}/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} {salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.dds.RData +{salmon,star_rsem,star_salmon}/deseq2_qc/R_sessionInfo.log {salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.pca.vals.txt {salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.plots.pdf {salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.sample.dists.txt diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 82632a9ed..3a80e40c1 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1384,7 +1384,6 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", @@ -1411,7 +1410,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index b5ec7924a..1eccfe27e 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -1349,7 +1349,6 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", @@ -1376,7 +1375,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 592344ef2..61c905b59 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1329,7 +1329,6 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 13f7db506..4868c9ac9 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -1115,7 +1115,6 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", @@ -1142,7 +1141,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", diff --git a/tests/nofasta.nf.test.snap b/tests/nofasta.nf.test.snap index 7653d7b9d..5808d1a2d 100644 --- a/tests/nofasta.nf.test.snap +++ b/tests/nofasta.nf.test.snap @@ -415,7 +415,6 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3e6d06d032abd3f5cd7e79df1b5bcde0", "lib_format_counts.json:md5,fce2c4840048c294c016f45f0df15384", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,1be389a28cc26d94b19ea918959ac72e" ] ], diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 10e04c209..8621eb648 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1300,7 +1300,6 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,fa7b659f1ba90e16b0d0a375ff318b01", "lib_format_counts.json:md5,e6e3d7746e9abee6a0e097ae0ee1781a", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,6cd02367152bb2dd59a6f1f70df2d7f8", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", @@ -1327,7 +1326,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,ddadea4a08511aae6faeb632eb6aafea", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,1db4c86723cf69052c4386760a9750bb", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc", diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 8411faa73..b1f4eb4b3 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -1164,7 +1164,6 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,4bf135c93c37f90c493f761f2709a28b", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,d1d3bd2a5617220b29a9063cb29f0578", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", @@ -1191,7 +1190,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,fdeebc4f056cbb52fee53e82c2e0096f", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,aa94a148bdbebec4e82cd18a00316506", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,bf065e266566c3fb96dc9319a3ed12cf", diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index da65d6b61..6ff1e2fca 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -1214,9 +1214,7 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8da31020df3c5b25167345609c6d08c5", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,3f269a6b2e9c8eaab66582e31d208dfc", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,7d96d6ddf1d12d43837b105865aeaafa", diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap index 9fd7a2f31..f57dddadd 100644 --- a/tests/umi.nf.test.snap +++ b/tests/umi.nf.test.snap @@ -1359,7 +1359,6 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,809380ddce725a8fab75dd7741b64bf6", "lib_format_counts.json:md5,d231ba7624b67eb654989f69530e2925", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,0f0e3687e731243392685c550fb1d93f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", @@ -1386,7 +1385,6 @@ "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,a3b1b764e21b500d9ffed5beb6da85ac", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,0b8c54ea7f2a78f7dd478a7bde53143e", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,ed386269dd82129149da4d33a9e0e0b6", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,ee34da4ee0f7b56c710f5df041f88f31", @@ -2713,7 +2711,6 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,809380ddce725a8fab75dd7741b64bf6", "lib_format_counts.json:md5,d231ba7624b67eb654989f69530e2925", - "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz:md5,e83d7f738fbbfaa541a2e71fe4663447", "RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz:md5,4f2873cbf584d6e84187238a4ae2b8fa",