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snapaligner: improve index detection (#1836)

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* improve index detection

* fix escaping
This commit is contained in:
Matthias De Smet 2022-06-30 12:19:46 +02:00 committed by GitHub
parent 253f8c1b0e
commit 44baf85bcc
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2 changed files with 7 additions and 7 deletions
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6
modules/snapaligner/align/main.nf
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@ -25,11 +25,11 @@ process SNAPALIGNER_ALIGN {
def subcmd = meta.single_end ? "single" : "paired" def subcmd = meta.single_end ? "single" : "paired"
""" """
mkdir -p index INDEX=`dirname \$(find -L ./ -name "OverflowTable*")`
mv $index index/ [ -z "\$INDEX" ] && echo "Snap index files not found" 1>&2 && exit 1
snap-aligner ${subcmd} \\ snap-aligner ${subcmd} \\
index \\ \$INDEX \\
${reads.join(" ")} \\ ${reads.join(" ")} \\
-o ${prefix}.bam \\ -o ${prefix}.bam \\
-t ${task.cpus} \\ -t ${task.cpus} \\

8
tests/modules/snapaligner/align/test.yml
View file

@ -5,9 +5,9 @@
- snapaligner - snapaligner
files: files:
- path: output/snapaligner/test.bam - path: output/snapaligner/test.bam
md5sum: 2dea536f28c041c1108add3523879243 md5sum: 9958e511fe759012cd11b7ef1f097639
- path: output/snapaligner/test.bam.bai - path: output/snapaligner/test.bam.bai
md5sum: 3f5cd1e8379b06554778a59b179ccc10 md5sum: f180c68a77445b317a22e3f1d6e6e114
- name: snapaligner align test_snapaligner_paired - name: snapaligner align test_snapaligner_paired
command: nextflow run ./tests/modules/snapaligner/align -entry test_snapaligner_paired -c ./tests/config/nextflow.config -c ./tests/modules/snapaligner/align/nextflow.config command: nextflow run ./tests/modules/snapaligner/align -entry test_snapaligner_paired -c ./tests/config/nextflow.config -c ./tests/modules/snapaligner/align/nextflow.config
@ -16,6 +16,6 @@
- snapaligner - snapaligner
files: files:
- path: output/snapaligner/test.bam - path: output/snapaligner/test.bam
md5sum: 941bf870355dd34ebe2ef43ea41abcc4 md5sum: cf656d5f18afa6a97825a685e1b2b141
- path: output/snapaligner/test.bam.bai - path: output/snapaligner/test.bam.bai
md5sum: ce7fd5bc6f0196e6ad70d3710e17e559 md5sum: fa2226d7f5b0b4b15d014332f94a8b84