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Commit 94e9ad17 authored by Xavier Grand's avatar Xavier Grand
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RNAseq_XGR, modif star:main_2.7.8a.nf input index val

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src/nf_modules/star/main_2.7.8a.nf
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...@@ -211,7 +211,7 @@ if (reads_id instanceof List){ ...@@ -211,7 +211,7 @@ if (reads_id instanceof List){
if (reads.size() == 2) if (reads.size() == 2)
""" """
STAR --runThreadN ${task.cpus} \ STAR --runThreadN ${task.cpus} \
--genomeDir ${index} \ --genomeDir $index \
--readFilesCommand zcat \ --readFilesCommand zcat \
--readFilesIn ${reads[0]} ${reads[1]} \ --readFilesIn ${reads[0]} ${reads[1]} \
--outFileNamePrefix ${reads_id}. \ --outFileNamePrefix ${reads_id}. \
...@@ -224,7 +224,7 @@ mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam ...@@ -224,7 +224,7 @@ mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam
else else
""" """
STAR --runThreadN ${task.cpus} \ STAR --runThreadN ${task.cpus} \
--genomeDir ${index} \ --genomeDir $index \
--readFilesCommand zcat \ --readFilesCommand zcat \
--readFilesIn ${reads} \ --readFilesIn ${reads} \
--outFileNamePrefix ${reads_id}. \ --outFileNamePrefix ${reads_id}. \
......
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