Verified Commit 451c10bb authored by Laurent Modolo's avatar Laurent Modolo
Browse files

alntools: try fix for bam bai

parent 972e601e
......@@ -21,6 +21,8 @@ process bam2ec {
script:
"""
cp ${bam} file_bam.bam
cp ${bam_idx} file_bam.bam.bai
awk -F"[\\t;]" '
\$3=="exon" {
ID=gensub(/transcript_id \\"(.*)\\"/, "\\\\1", "g", \$11);
......@@ -31,6 +33,6 @@ END{
{print i"\\t"LEN[i]}
}
' ${gtf} > ${gtf.simpleName}_transcripts_lengths.tsv
alntools bam2ec ${params.bam2ec} -t ${gtf.simpleName}_transcripts_lengths.tsv ${bam} ${bam.simpleName}.bin
alntools bam2ec ${params.bam2ec} -t ${gtf.simpleName}_transcripts_lengths.tsv file_bam.bam ${bam.simpleName}.bin
"""
}
\ No newline at end of file
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