From 24707f2144aff3e966827376f37fb990fe0aa92e Mon Sep 17 00:00:00 2001 From: Maxime Borry Date: Wed, 10 Nov 2021 13:21:12 +0100 Subject: [PATCH] Fix read indexing in AdapterRemoval module (#1051) * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates * add optional inputs/outpus * remove trailing whitespace * compressing and removing not reproducible md5sums * follow symlinks while decompressing * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates * split tests * export env variable * Update modules/metabat2/jgisummarizebamcontigdepths/main.nf Co-authored-by: James A. Fellows Yates * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates * Update modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates * answer PR comments and switch to bgzip * fix read index * update test.yml Co-authored-by: James A. Fellows Yates Co-authored-by: Harshil Patel Co-authored-by: Gregor Sturm --- modules/adapterremoval/main.nf | 4 ++-- tests/modules/adapterremoval/test.yml | 12 ++++++------ 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/adapterremoval/main.nf b/modules/adapterremoval/main.nf index fad3963f..6d559826 100644 --- a/modules/adapterremoval/main.nf +++ b/modules/adapterremoval/main.nf @@ -49,7 +49,7 @@ process ADAPTERREMOVAL { """ AdapterRemoval \\ --file1 ${reads[0]} \\ - --file2 ${reads[0]} \\ + --file2 ${reads[1]} \\ $options.args \\ --basename $prefix \\ --threads $task.cpus \\ @@ -68,7 +68,7 @@ process ADAPTERREMOVAL { """ AdapterRemoval \\ --file1 ${reads[0]} \\ - --file2 ${reads[0]} \\ + --file2 ${reads[1]} \\ --collapse \\ $options.args \\ --basename $prefix \\ diff --git a/tests/modules/adapterremoval/test.yml b/tests/modules/adapterremoval/test.yml index 95cd4b04..318e7866 100644 --- a/tests/modules/adapterremoval/test.yml +++ b/tests/modules/adapterremoval/test.yml @@ -13,12 +13,12 @@ tags: - adapterremoval files: - - path: output/adapterremoval/test.pair2.trimmed.fastq.gz - md5sum: f076a9f666235e01a3281f8c46c9d010 - path: output/adapterremoval/test.log - md5sum: bea86105aff4d27fe29c83e24498fefa + md5sum: b8a451d3981b327f3fdb44f40ba2d6d1 - path: output/adapterremoval/test.pair1.trimmed.fastq.gz - md5sum: f076a9f666235e01a3281f8c46c9d010 + md5sum: 294a6277f0139bd597e57c6fa31f39c7 + - path: output/adapterremoval/test.pair2.trimmed.fastq.gz + md5sum: de7b38e2c881bced8671acb1ab452d78 - name: adapterremoval test_adapterremoval_paired_end_collapse command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config @@ -26,6 +26,6 @@ - adapterremoval files: - path: output/adapterremoval/test.log - md5sum: 97cb97b3d03123ac88430768b2e36c59 + md5sum: 7f0b2328152226e46101a535cce718b3 - path: output/adapterremoval/test.merged.fastq.gz - md5sum: 50a4f9fdac6a24e211eb4dcf9f292bef + md5sum: 07a8f725bfd3ecbeabdc41b32d898dee