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Fix homer/maketagdirectory output collision (#1456)

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* fix(homer): Update tagdir to have a prefix

Otherwise they have a naming collision

* test(homer): Update paths

* style(homer): Align ,'s

* chore(homer): Update md5sums
This commit is contained in:
Edmund Miller 2022-03-26 22:17:42 -05:00 committed by GitHub
parent 5acf301ddd
commit 5832fbc225
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GPG key ID: 4AEE18F83AFDEB23
5 changed files with 31 additions and 26 deletions
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5
modules/homer/maketagdirectory/main.nf
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@ -14,7 +14,8 @@ process HOMER_MAKETAGDIRECTORY {
path fasta path fasta
output: output:
tuple val(meta), path("tag_dir"), emit: tagdir tuple val(meta), path("*_tagdir") , emit: tagdir
tuple val(meta), path("*_tagdir/tagInfo.txt"), emit: taginfo
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -25,7 +26,7 @@ process HOMER_MAKETAGDIRECTORY {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
makeTagDirectory \\ makeTagDirectory \\
tag_dir \\ ${prefix}_tagdir \\
-genome $fasta \\ -genome $fasta \\
$args \\ $args \\
$bam $bam

8
modules/homer/maketagdirectory/meta.yml
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@ -57,10 +57,14 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- tag_dir: - tagdir:
type: directory type: directory
description: The "Tag Directory" description: The "Tag Directory"
pattern: "tag_dir" pattern: "*_tagdir"
- taginfo:
type: directory
description: The tagInfo.txt included to ensure there's proper output
pattern: "*_tagdir/tagInfo.txt"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions

2
tests/modules/homer/findpeaks/test.yml
View file

@ -5,4 +5,4 @@
- homer/findpeaks - homer/findpeaks
files: files:
- path: output/homer/test.peaks.txt - path: output/homer/test.peaks.txt
md5sum: f75ac1fea67f1e307a1ad4d059a9b6cc md5sum: 86e15beaa4b439585786478e58418c0c

36
tests/modules/homer/maketagdirectory/test.yml
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@ -4,15 +4,15 @@
- homer - homer
- homer/maketagdirectory - homer/maketagdirectory
files: files:
- path: output/homer/tag_dir/MT192765.1.tags.tsv - path: output/homer/test_tagdir/MT192765.1.tags.tsv
md5sum: e29522171ca2169b57396495f8b97485 md5sum: e29522171ca2169b57396495f8b97485
- path: output/homer/tag_dir/tagAutocorrelation.txt - path: output/homer/test_tagdir/tagAutocorrelation.txt
md5sum: 62b107c4971b94126fb89a0bc2800455 md5sum: 62b107c4971b94126fb89a0bc2800455
- path: output/homer/tag_dir/tagCountDistribution.txt - path: output/homer/test_tagdir/tagCountDistribution.txt
md5sum: fd4ee7ce7c5dfd7c9d739534b8180578 md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
- path: output/homer/tag_dir/tagInfo.txt - path: output/homer/test_tagdir/tagInfo.txt
md5sum: ff56f30411b221b847aa4e6e9a6098a1 md5sum: c9bb2ca53bb101d74c1ec92d2b0ad26e
- path: output/homer/tag_dir/tagLengthDistribution.txt - path: output/homer/test_tagdir/tagLengthDistribution.txt
md5sum: e5aa2b9843ca9c04ace297280aed6af4 md5sum: e5aa2b9843ca9c04ace297280aed6af4
- name: homer maketagdirectory meta - name: homer maketagdirectory meta
@ -21,15 +21,15 @@
- homer - homer
- homer/maketagdirectory - homer/maketagdirectory
files: files:
- path: output/homer/tag_dir/MT192765.1.tags.tsv - path: output/homer/meta_test_tagdir/MT192765.1.tags.tsv
md5sum: e29522171ca2169b57396495f8b97485 md5sum: e29522171ca2169b57396495f8b97485
- path: output/homer/tag_dir/tagAutocorrelation.txt - path: output/homer/meta_test_tagdir/tagAutocorrelation.txt
md5sum: 62b107c4971b94126fb89a0bc2800455 md5sum: 62b107c4971b94126fb89a0bc2800455
- path: output/homer/tag_dir/tagCountDistribution.txt - path: output/homer/meta_test_tagdir/tagCountDistribution.txt
md5sum: fd4ee7ce7c5dfd7c9d739534b8180578 md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
- path: output/homer/tag_dir/tagInfo.txt - path: output/homer/meta_test_tagdir/tagInfo.txt
md5sum: ff56f30411b221b847aa4e6e9a6098a1 md5sum: cb907ebf9afc042bb61196d624e793c8
- path: output/homer/tag_dir/tagLengthDistribution.txt - path: output/homer/meta_test_tagdir/tagLengthDistribution.txt
md5sum: e5aa2b9843ca9c04ace297280aed6af4 md5sum: e5aa2b9843ca9c04ace297280aed6af4
- name: homer maketagdirectory bam - name: homer maketagdirectory bam
@ -38,13 +38,13 @@
- homer - homer
- homer/maketagdirectory - homer/maketagdirectory
files: files:
- path: output/homer/tag_dir/MT192765.1.tags.tsv - path: output/homer/test_tagdir/MT192765.1.tags.tsv
md5sum: 365808c4751ef6dd7085ac52037a22bc md5sum: 365808c4751ef6dd7085ac52037a22bc
- path: output/homer/tag_dir/tagAutocorrelation.txt - path: output/homer/test_tagdir/tagAutocorrelation.txt
md5sum: 8b396f2aef1cdd3af4fab57b142d3250 md5sum: 8b396f2aef1cdd3af4fab57b142d3250
- path: output/homer/tag_dir/tagCountDistribution.txt - path: output/homer/test_tagdir/tagCountDistribution.txt
md5sum: afc6d007096c3872bbe84c9dc8edb832 md5sum: afc6d007096c3872bbe84c9dc8edb832
- path: output/homer/tag_dir/tagInfo.txt - path: output/homer/test_tagdir/tagInfo.txt
md5sum: fbaf46eeb8a0723fa8b5eabd93f9d821 md5sum: aebf6ff15fd0a238ee6a94d623c578ca
- path: output/homer/tag_dir/tagLengthDistribution.txt - path: output/homer/test_tagdir/tagLengthDistribution.txt
md5sum: 44f231adb2a705ae81950808c55cf248 md5sum: 44f231adb2a705ae81950808c55cf248

4
tests/modules/homer/pos2bed/test.yml
View file

@ -4,7 +4,7 @@
- "homer" - "homer"
- "homer/pos2bed" - "homer/pos2bed"
files: files:
- path: "output/homer/test.bed" - path: output/homer/test.bed
md5sum: 0b9ebd8f06b9c820a551fbdb2d7635ee md5sum: 5d6ddd9c7e621a66f6f045b9b5abecb4
- path: output/homer/versions.yml - path: output/homer/versions.yml
md5sum: 1485f4b2d76484e8fe3310e2505de2fd md5sum: 1485f4b2d76484e8fe3310e2505de2fd