From a46d7b844b826f8ca3e23be5b0cec12696974766 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Felix=20M=C3=B6lder?= Date: Thu, 13 Oct 2022 08:22:20 +0200 Subject: [PATCH] fix: set RG tag --- .../meta.yaml | 0 .../test/Snakefile | 1 + .../test/mapped/sampleA.marked.bam | Bin .../test/resources/genome.fa | 0 .../test/resources/genome.fa.amb | 0 .../test/resources/genome.fa.ann | 0 .../test/resources/genome.fa.bwt | Bin .../test/resources/genome.fa.pac | Bin .../test/resources/genome.fa.sa | Bin .../used_wrappers.yaml | 0 test.py | 2 +- 11 files changed, 2 insertions(+), 1 deletion(-) rename meta/bio/{rbt_calc_consensus => calc_consensus_reads}/meta.yaml (100%) rename meta/bio/{rbt_calc_consensus => calc_consensus_reads}/test/Snakefile (98%) rename meta/bio/{rbt_calc_consensus => calc_consensus_reads}/test/mapped/sampleA.marked.bam (100%) rename meta/bio/{rbt_calc_consensus => calc_consensus_reads}/test/resources/genome.fa (100%) rename meta/bio/{rbt_calc_consensus => calc_consensus_reads}/test/resources/genome.fa.amb (100%) rename meta/bio/{rbt_calc_consensus => calc_consensus_reads}/test/resources/genome.fa.ann (100%) rename meta/bio/{rbt_calc_consensus => calc_consensus_reads}/test/resources/genome.fa.bwt (100%) rename meta/bio/{rbt_calc_consensus => calc_consensus_reads}/test/resources/genome.fa.pac (100%) rename meta/bio/{rbt_calc_consensus => calc_consensus_reads}/test/resources/genome.fa.sa (100%) rename meta/bio/{rbt_calc_consensus => calc_consensus_reads}/used_wrappers.yaml (100%) diff --git a/meta/bio/rbt_calc_consensus/meta.yaml b/meta/bio/calc_consensus_reads/meta.yaml similarity index 100% rename from meta/bio/rbt_calc_consensus/meta.yaml rename to meta/bio/calc_consensus_reads/meta.yaml diff --git a/meta/bio/rbt_calc_consensus/test/Snakefile b/meta/bio/calc_consensus_reads/test/Snakefile similarity index 98% rename from meta/bio/rbt_calc_consensus/test/Snakefile rename to meta/bio/calc_consensus_reads/test/Snakefile index c67346e17e6..f1df2b95629 100644 --- a/meta/bio/rbt_calc_consensus/test/Snakefile +++ b/meta/bio/calc_consensus_reads/test/Snakefile @@ -29,6 +29,7 @@ rule map_consensus_reads: output: temp("results/consensus_mapped/{sample}.{read_type}.bam"), params: + extra=r"-R '@RG\tID:{sample}\tSM:{sample}'", index=lambda w, input: os.path.splitext(input.idx[0])[0], sort="samtools", sort_order="coordinate", diff --git a/meta/bio/rbt_calc_consensus/test/mapped/sampleA.marked.bam b/meta/bio/calc_consensus_reads/test/mapped/sampleA.marked.bam similarity index 100% rename from meta/bio/rbt_calc_consensus/test/mapped/sampleA.marked.bam rename to meta/bio/calc_consensus_reads/test/mapped/sampleA.marked.bam diff --git a/meta/bio/rbt_calc_consensus/test/resources/genome.fa b/meta/bio/calc_consensus_reads/test/resources/genome.fa similarity index 100% rename from meta/bio/rbt_calc_consensus/test/resources/genome.fa rename to meta/bio/calc_consensus_reads/test/resources/genome.fa diff --git a/meta/bio/rbt_calc_consensus/test/resources/genome.fa.amb b/meta/bio/calc_consensus_reads/test/resources/genome.fa.amb similarity index 100% rename from meta/bio/rbt_calc_consensus/test/resources/genome.fa.amb rename to meta/bio/calc_consensus_reads/test/resources/genome.fa.amb diff --git a/meta/bio/rbt_calc_consensus/test/resources/genome.fa.ann b/meta/bio/calc_consensus_reads/test/resources/genome.fa.ann similarity index 100% rename from meta/bio/rbt_calc_consensus/test/resources/genome.fa.ann rename to meta/bio/calc_consensus_reads/test/resources/genome.fa.ann diff --git a/meta/bio/rbt_calc_consensus/test/resources/genome.fa.bwt b/meta/bio/calc_consensus_reads/test/resources/genome.fa.bwt similarity index 100% rename from meta/bio/rbt_calc_consensus/test/resources/genome.fa.bwt rename to meta/bio/calc_consensus_reads/test/resources/genome.fa.bwt diff --git a/meta/bio/rbt_calc_consensus/test/resources/genome.fa.pac b/meta/bio/calc_consensus_reads/test/resources/genome.fa.pac similarity index 100% rename from meta/bio/rbt_calc_consensus/test/resources/genome.fa.pac rename to meta/bio/calc_consensus_reads/test/resources/genome.fa.pac diff --git a/meta/bio/rbt_calc_consensus/test/resources/genome.fa.sa b/meta/bio/calc_consensus_reads/test/resources/genome.fa.sa similarity index 100% rename from meta/bio/rbt_calc_consensus/test/resources/genome.fa.sa rename to meta/bio/calc_consensus_reads/test/resources/genome.fa.sa diff --git a/meta/bio/rbt_calc_consensus/used_wrappers.yaml b/meta/bio/calc_consensus_reads/used_wrappers.yaml similarity index 100% rename from meta/bio/rbt_calc_consensus/used_wrappers.yaml rename to meta/bio/calc_consensus_reads/used_wrappers.yaml diff --git a/test.py b/test.py index 5148b7e5d05..3b4304f8996 100644 --- a/test.py +++ b/test.py @@ -4851,6 +4851,6 @@ def test_collapse_reads_to_fragments_bam(): @skip_if_not_modified def test_calc_consensus_reads(): run( - "meta/bio/rbt_calc_consensus/", + "meta/bio/calc_consensus_reads/", ["snakemake", "--cores", "1", "--use-conda", "-F", "results/consensus/sampleA.bam"], ) \ No newline at end of file