From 56d5eb983463e74047acc2e1c81346715519c7fb Mon Sep 17 00:00:00 2001 From: Maxime Borry Date: Wed, 10 Nov 2021 17:40:07 +0100 Subject: [PATCH] Add Bacillus fragilis alignments to `test_data.config` (#1054) * 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 * add bacillus fragilis alignments Co-authored-by: James A. Fellows Yates Co-authored-by: Harshil Patel Co-authored-by: Gregor Sturm --- tests/config/test_data.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 6cb494f7..c34696f2 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -267,6 +267,12 @@ params { test1_2_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz" test2_1_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz" test2_2_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz" + test1_paired_end_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test1.bam" + test1_paired_end_sorted_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test1.sorted.bam" + test1_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai" + test2_paired_end_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test2.bam" + test2_paired_end_sorted_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test2.sorted.bam" + test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai" } 'nanopore' { test_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/nanopore/fastq/test.fastq.gz"