From 0a5ddd0ad0f3035253fab569caa631fa0a81db9b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Guizard?= Date: Sat, 23 Oct 2021 19:39:27 +0100 Subject: [PATCH] Update module: `bamtools/split` (#885) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update with new versions.yml file * 🐛 FIX: Update meta.yml + correct typos * Update modules/bamtools/split/meta.yml Add bam, split, chunk tags Co-authored-by: James A. Fellows Yates * 🐛 FIX: Correct meta.yml * 🐛 FIX: Grab software name using ${getSoftwareName(task.process)} * 🐛 FIX: Update test.yml Co-authored-by: James A. Fellows Yates Co-authored-by: Harshil Patel --- modules/bamtools/split/main.nf | 2 +- tests/modules/bamtools/split/test.yml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf index 506a957c..86eaa5d6 100644 --- a/modules/bamtools/split/main.nf +++ b/modules/bamtools/split/main.nf @@ -35,7 +35,7 @@ process BAMTOOLS_SPLIT { cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: - bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' ) + ${getSoftwareName(task.process)}: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' ) END_VERSIONS """ } diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml index f92f9345..f28a9bcf 100644 --- a/tests/modules/bamtools/split/test.yml +++ b/tests/modules/bamtools/split/test.yml @@ -1,10 +1,10 @@ - name: bamtools split test_bamtools_split command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split -c tests/config/nextflow.config tags: - - bamtools - bamtools/split + - bamtools files: - - path: output/bamtools/test.paired_end.sorted.REF_chr22:16570000-16610000.bam - md5sum: 256535b9a3ab5864be0f7dea2218d159 + - path: output/bamtools/test.paired_end.sorted.REF_chr22.bam + md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07 - path: output/bamtools/test.paired_end.sorted.REF_unmapped.bam - md5sum: 568e058d871d8bc319330360bcae4e43 + md5sum: e0754bf72c51543b2d745d96537035fb