From a59a6f3b761737496bde271cce547ca95451a5bb Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 3 Jan 2024 15:01:33 +0000 Subject: [PATCH 1/3] Patch modules to fix #1103 --- modules.json | 12 ++++--- modules/nf-core/fastp/fastp.diff | 32 +++++++++++++++++++ modules/nf-core/fastp/main.nf | 6 ++-- modules/nf-core/fastqc/fastqc.diff | 23 +++++++++++++ modules/nf-core/fastqc/main.nf | 4 +-- modules/nf-core/umitools/dedup/main.nf | 4 +-- .../umitools/dedup/umitools-dedup.diff | 23 +++++++++++++ modules/nf-core/umitools/extract/main.nf | 4 +-- .../umitools/extract/umitools-extract.diff | 23 +++++++++++++ 9 files changed, 118 insertions(+), 13 deletions(-) create mode 100644 modules/nf-core/fastp/fastp.diff create mode 100644 modules/nf-core/fastqc/fastqc.diff create mode 100644 modules/nf-core/umitools/dedup/umitools-dedup.diff create mode 100644 modules/nf-core/umitools/extract/umitools-extract.diff diff --git a/modules.json b/modules.json index e78ca060c..d22e252fe 100644 --- a/modules.json +++ b/modules.json @@ -28,12 +28,14 @@ "fastp": { "branch": "master", "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd", - "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] + "installed_by": ["fastq_fastqc_umitools_fastp", "modules"], + "patch": "modules/nf-core/fastp/fastp.diff" }, "fastqc": { "branch": "master", "git_sha": "102cc9b709a6da9f7cee2373563ab1464fca9c0a", - "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"] + "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"], + "patch": "modules/nf-core/fastqc/fastqc.diff" }, "fq/subsample": { "branch": "master", @@ -222,12 +224,14 @@ "umitools/dedup": { "branch": "master", "git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd", - "installed_by": ["bam_dedup_stats_samtools_umitools"] + "installed_by": ["bam_dedup_stats_samtools_umitools"], + "patch": "modules/nf-core/umitools/dedup/umitools-dedup.diff" }, "umitools/extract": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] + "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"], + "patch": "modules/nf-core/umitools/extract/umitools-extract.diff" }, "untar": { "branch": "master", diff --git a/modules/nf-core/fastp/fastp.diff b/modules/nf-core/fastp/fastp.diff new file mode 100644 index 000000000..b50d8e387 --- /dev/null +++ b/modules/nf-core/fastp/fastp.diff @@ -0,0 +1,32 @@ +Changes in module 'nf-core/fastp' +--- modules/nf-core/fastp/main.nf ++++ modules/nf-core/fastp/main.nf +@@ -45,7 +45,7 @@ + $adapter_list \\ + $fail_fastq \\ + $args \\ +- 2> ${prefix}.fastp.log \\ ++ 2> >(tee ${prefix}.fastp.log >&2) \\ + | gzip -c > ${prefix}.fastp.fastq.gz + + cat <<-END_VERSIONS > versions.yml +@@ -66,7 +66,7 @@ + $adapter_list \\ + $fail_fastq \\ + $args \\ +- 2> ${prefix}.fastp.log ++ 2> >(tee ${prefix}.fastp.log >&2) + + cat <<-END_VERSIONS > versions.yml + "${task.process}": +@@ -91,7 +91,7 @@ + --thread $task.cpus \\ + --detect_adapter_for_pe \\ + $args \\ +- 2> ${prefix}.fastp.log ++ 2> >(tee ${prefix}.fastp.log >&2) + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + +************************************************************ diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 831b7f128..8cade07f0 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -45,7 +45,7 @@ process FASTP { $adapter_list \\ $fail_fastq \\ $args \\ - 2> ${prefix}.fastp.log \\ + 2> >(tee ${prefix}.fastp.log >&2) \\ | gzip -c > ${prefix}.fastp.fastq.gz cat <<-END_VERSIONS > versions.yml @@ -66,7 +66,7 @@ process FASTP { $adapter_list \\ $fail_fastq \\ $args \\ - 2> ${prefix}.fastp.log + 2> >(tee ${prefix}.fastp.log >&2) cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -91,7 +91,7 @@ process FASTP { --thread $task.cpus \\ --detect_adapter_for_pe \\ $args \\ - 2> ${prefix}.fastp.log + 2> >(tee ${prefix}.fastp.log >&2) cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/fastqc/fastqc.diff b/modules/nf-core/fastqc/fastqc.diff new file mode 100644 index 000000000..0518d2b8f --- /dev/null +++ b/modules/nf-core/fastqc/fastqc.diff @@ -0,0 +1,23 @@ +Changes in module 'nf-core/fastqc' +--- modules/nf-core/fastqc/main.nf ++++ modules/nf-core/fastqc/main.nf +@@ -37,7 +37,7 @@ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": +- fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) ++ fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) + END_VERSIONS + """ + +@@ -49,7 +49,7 @@ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": +- fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) ++ fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) + END_VERSIONS + """ + } + +************************************************************ diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 67209f793..c9f64702b 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -37,7 +37,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ @@ -49,7 +49,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ } diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index 56ea04691..824ebeeb3 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -42,7 +42,7 @@ process UMITOOLS_DEDUP { cat <<-END_VERSIONS > versions.yml "${task.process}": - umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') + umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) END_VERSIONS """ @@ -56,7 +56,7 @@ process UMITOOLS_DEDUP { cat <<-END_VERSIONS > versions.yml "${task.process}": - umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') + umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) END_VERSIONS """ } 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..327583445 --- /dev/null +++ b/modules/nf-core/umitools/dedup/umitools-dedup.diff @@ -0,0 +1,23 @@ +Changes in module 'nf-core/umitools/dedup' +--- modules/nf-core/umitools/dedup/main.nf ++++ modules/nf-core/umitools/dedup/main.nf +@@ -42,7 +42,7 @@ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": +- umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') ++ umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) + END_VERSIONS + """ + +@@ -56,7 +56,7 @@ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": +- umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') ++ umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) + END_VERSIONS + """ + } + +************************************************************ diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 2f94fa93e..5ffe4eb76 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -33,7 +33,7 @@ process UMITOOLS_EXTRACT { cat <<-END_VERSIONS > versions.yml "${task.process}": - umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') + umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) END_VERSIONS """ } else { @@ -49,7 +49,7 @@ process UMITOOLS_EXTRACT { cat <<-END_VERSIONS > versions.yml "${task.process}": - umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') + umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) END_VERSIONS """ } 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..464a23c00 --- /dev/null +++ b/modules/nf-core/umitools/extract/umitools-extract.diff @@ -0,0 +1,23 @@ +Changes in module 'nf-core/umitools/extract' +--- modules/nf-core/umitools/extract/main.nf ++++ modules/nf-core/umitools/extract/main.nf +@@ -33,7 +33,7 @@ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": +- umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') ++ umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) + END_VERSIONS + """ + } else { +@@ -49,7 +49,7 @@ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": +- umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') ++ umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) + END_VERSIONS + """ + } + +************************************************************ From 0bb288a7f644221ec77eeda70b4e193e6947f7d3 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 3 Jan 2024 15:39:41 +0000 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d6544378a..1a8ce9bf6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements & fixes - [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling. +- [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Patch modules to fix #1103 ### Software dependencies From b6a2d529fc34e797f240ba44ae1f47637ede97bb Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 3 Jan 2024 16:44:40 +0100 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1a8ce9bf6..4ad8ceab7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,14 +7,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Credits -### Enhancements & fixes +Special thanks to the following for their contributions to the release: -- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling. -- [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Patch modules to fix #1103 +- [Adam Talbot](https://github.com/adamrtalbot) +- [Jonathan Manning](https://github.com/pinin4fjords) +- [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal) +- [Matthias Zepper](https://github.com/MatthiasZepper) +- [Maxime Garcia](https://github.com/maxulysse) +- [Phil Ewels](https://github.com/ewels) +- [Vlad Savelyev](https://github.com/vladsavelyev) -### Software dependencies +### Enhancements & fixes -### Modules / Subworkflows +- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling +- [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Fix and patch version commands for Fastp, FastQC and UMI-tools modules ([#1103](https://github.com/nf-core/rnaseq/issues/1103)) ## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21