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add stub for stringtie (#1949)

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* add stub for stringtie

* add ballgown file to test.yml

* add ballgown file to test.yml forward
This commit is contained in:
Annick Renevey 2022-08-09 10:11:37 +02:00 committed by GitHub
parent cd22a76c78
commit 47cc7a77bf
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4 changed files with 68 additions and 0 deletions
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10
modules/stringtie/merge/main.nf
View file

@ -31,4 +31,14 @@ process STRINGTIE_MERGE {
stringtie: \$(stringtie --version 2>&1) stringtie: \$(stringtie --version 2>&1)
END_VERSIONS END_VERSIONS
""" """
stub:
"""
touch stringtie.merged.gtf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
stringtie: \$(stringtie --version 2>&1)
END_VERSIONS
"""
} }

14
modules/stringtie/stringtie/main.nf
View file

@ -48,4 +48,18 @@ process STRINGTIE_STRINGTIE {
stringtie: \$(stringtie --version 2>&1) stringtie: \$(stringtie --version 2>&1)
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.transcripts.gtf
touch ${prefix}.gene.abundance.txt
touch ${prefix}.coverage.gtf
touch ${prefix}.ballgown
cat <<-END_VERSIONS > versions.yml
"${task.process}":
stringtie: \$(stringtie --version 2>&1)
END_VERSIONS
"""
} }

22
tests/modules/stringtie/merge/test.yml
View file

@ -45,3 +45,25 @@
md5sum: f289f41b3ba1b9f0aa05d14408f1a5da md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
- path: output/stringtie/test.transcripts.gtf - path: output/stringtie/test.transcripts.gtf
md5sum: 9dcdc9577c0fdbb25089eda210267546 md5sum: 9dcdc9577c0fdbb25089eda210267546
- name: stringtie merge forward-strand stub
command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config -stub-run
tags:
- stringtie
- stringtie/merge
files:
- path: output/stringtie/stringtie.merged.gtf
- path: output/stringtie/test.coverage.gtf
- path: output/stringtie/test.gene.abundance.txt
- path: output/stringtie/test.transcripts.gtf
- name: stringtie merge test_stringtie_reverse_merge stub
command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config -stub-run
tags:
- stringtie
- stringtie/merge
files:
- path: output/stringtie/stringtie.merged.gtf
- path: output/stringtie/test.coverage.gtf
- path: output/stringtie/test.gene.abundance.txt
- path: output/stringtie/test.transcripts.gtf

22
tests/modules/stringtie/stringtie/test.yml
View file

@ -39,3 +39,25 @@
md5sum: 8a117c8aa4334b4c2d4711932b006fb4 md5sum: 8a117c8aa4334b4c2d4711932b006fb4
- path: ./output/stringtie/test.ballgown/e2t.ctab - path: ./output/stringtie/test.ballgown/e2t.ctab
md5sum: e981c0038295ae54b63cedb1083f1540 md5sum: e981c0038295ae54b63cedb1083f1540
- name: stringtie stringtie forward stub
command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_forward -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config -stub-run
tags:
- stringtie
- stringtie/stringtie
files:
- path: ./output/stringtie/test.transcripts.gtf
- path: ./output/stringtie/test.gene.abundance.txt
- path: ./output/stringtie/test.coverage.gtf
- path: ./output/stringtie/test.ballgown
- name: stringtie stringtie reverse stub
command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_reverse -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config -stub-run
tags:
- stringtie
- stringtie/stringtie
files:
- path: ./output/stringtie/test.transcripts.gtf
- path: ./output/stringtie/test.gene.abundance.txt
- path: ./output/stringtie/test.coverage.gtf
- path: ./output/stringtie/test.ballgown