diff --git a/src/.docker_modules/htseq/0.13.5/Dockerfile b/src/.docker_modules/htseq/0.13.5/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..68347cf4a63723c11b3a7e4d01817c6ef8d18f79 --- /dev/null +++ b/src/.docker_modules/htseq/0.13.5/Dockerfile @@ -0,0 +1,2 @@ +FROM quay.io/biocontainers/htseq:0.13.5--py39h70b41aa_1 +MAINTAINER Laurent Modolo diff --git a/src/.docker_modules/htseq/0.13.5/docker_init.sh b/src/.docker_modules/htseq/0.13.5/docker_init.sh new file mode 100755 index 0000000000000000000000000000000000000000..ca03fe9af2bc8f9f2bb9d70efc02a0c01e40cfde --- /dev/null +++ b/src/.docker_modules/htseq/0.13.5/docker_init.sh @@ -0,0 +1,4 @@ +#!/bin/sh +docker pull lbmc/htseq:0.13.5 +docker build src/.docker_modules/htseq/0.13.5 -t 'lbmc/htseq:0.13.5' +docker push lbmc/htseq:0.13.5 diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf index 6bb6d764ff5488e5bc31539833e3f50bd43a1e7f..5110b222d91721ed85d83f1240838b6cb5ce3b2b 100644 --- a/src/nf_modules/kb/main.nf +++ b/src/nf_modules/kb/main.nf @@ -147,6 +147,7 @@ process kb_default { -x 10XV3 \ ${params.count} \ ${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt + cp ${transcript_to_gene} ${file_prefix}/ """ } @@ -196,6 +197,7 @@ process kb_marseq { ${params.count} \ -x 1,0,6:1,6,14:0,0,0 \ ${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt + cp ${transcript_to_gene} ${file_prefix}/ """ else """ @@ -209,6 +211,7 @@ process kb_marseq { ${params.count} \ -x 1,0,6:1,6,14:0,0,0 \ ${reads} > ${file_prefix}_kb_mapping_report.txt + cp ${transcript_to_gene} ${file_prefix}/ """ } @@ -335,6 +338,9 @@ process velocity_default { -x 10XV3 \ ${params.count} \ ${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt + cp ${transcript_to_gene} ${file_prefix}/ + cp ${cdna_t2g} ${file_prefix}/ + cp ${intron_t2g} ${file_prefix}/ """ } @@ -387,6 +393,9 @@ process velocity_marseq { ${params.count} \ -x 1,0,6:1,6,14:0,0,0 \ ${reads[0]} ${reads[1]} > ${file_prefix}_kb_mapping_report.txt + cp ${transcript_to_gene} ${file_prefix}/ + cp ${cdna_t2g} ${file_prefix}/ + cp ${intron_t2g} ${file_prefix}/ """ else """ @@ -403,5 +412,8 @@ process velocity_marseq { ${params.count} \ -x 1,0,6:1,6,14:0,0,0 \ ${reads} > ${file_prefix}_kb_mapping_report.txt + cp ${transcript_to_gene} ${file_prefix}/ + cp ${cdna_t2g} ${file_prefix}/ + cp ${intron_t2g} ${file_prefix}/ """ } \ No newline at end of file