Verified Commit 5a367584 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

kb: fix missing \ at end of lines

parent fdb6eac6
......@@ -44,7 +44,10 @@ process tr2g {
if (t2g_id == "NO T2G")
"""
t2g.py --gtf ${gtf}
t2g.py --gtf ${gtf} && \
mv t2g.txt t2g_to_fix.txt && \
sed -E 's/\\.[0-9]+//g' t2g_to_fix.txt | \
awk '{print(\$1 "\\t" \$2)}' > t2g.txt
"""
else
"""
......@@ -102,12 +105,12 @@ workflow count {
switch(params.kb_protocol) {
case "marsseq":
split(fastq, config)
kb_marseq(index.collect(), split.out.fastq, transcript_to_gene, whitelist_optional)
kb_marseq(index.collect(), split.out.fastq, transcript_to_gene.collect(), whitelist_optional.collect())
kb_marseq.out.counts.set{res_counts}
kb_marseq.out.report.set{res_report}
break;
default:
kb_default(index, fastq, transcript_to_gene, whitelist_optional)
kb_default(index.collect(), fastq, transcript_to_gene.collect(), whitelist_optional.collect())
kb_default.out.counts.set{res_counts}
kb_default.out.report.set{res_report}
break;
......@@ -155,11 +158,11 @@ process kb_default {
-m ${kb_memory} \
-i ${index} \
-g ${transcript_to_gene} \
-o ${file_prefix} \
${whitelist_param} \
-x 10XV3
-x 10XV3 \
${params.count} \
-o ${file_prefix} \
${reads[0]} ${reads[1]} &> ${file_prefix}_kb_mapping_report.txt
${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt
"""
}
......@@ -204,11 +207,11 @@ process kb_marseq {
-m ${kb_memory} \
-i ${index} \
-g ${transcript_to_gene} \
-o ${file_prefix} \
${whitelist_param} \
${params.count} \
-x 1,0,6:1,6,14:1,14,0
-o ${file_prefix} \
${reads[0]} ${reads[1]} &> ${file_prefix}_kb_mapping_report.txt
-x 1,0,6:1,6,14:1,14,0 \
${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt
"""
else
"""
......@@ -217,10 +220,10 @@ process kb_marseq {
-m ${kb_memory} \
-i ${index} \
-g ${transcript_to_gene} \
-o ${file_prefix} \
${whitelist_param} \
${params.count} \
-x 1,0,6:1,6,14:1,14,0
-o ${file_prefix} \
${reads} &> ${file_prefix}_kb_mapping_report.txt
-x 1,0,6:1,6,14:1,14,0 \
${reads} > ${file_prefix}_kb_mapping_report.txt
"""
}
\ No newline at end of file
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