From bede4d3ad9ce9ddf4987983ff31a1acd1d93b245 Mon Sep 17 00:00:00 2001 From: Steven Leonard Date: Mon, 11 Feb 2019 10:56:44 +0000 Subject: [PATCH 1/3] fixed Not enough reads to run Salmon check --- data/vtlib/salmon_alignment.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/data/vtlib/salmon_alignment.json b/data/vtlib/salmon_alignment.json index 2fdcea13f..92dca6b1e 100644 --- a/data/vtlib/salmon_alignment.json +++ b/data/vtlib/salmon_alignment.json @@ -99,14 +99,14 @@ "--geneMap", {"subst":"annotation_val", "required":"yes"}, "--output", {"subst":"salmon_out"}, {"subst":"b2c_mt", "ifnull":{"subst_constructor":{ "vals":[ "-p", {"subst":"b2c_mt_val"} ]}}}, "\";", - "case `file $0` in *ASCII*) PART1=`head -c 50K $0 | wc -l`;; *compressed*) PART1=`gunzip -c $0 | head -c 50K | wc -l`;; *empty*) PART1=0;; esac;", + "case `file $0` in *ASCII*) PART1=`head -n 1000 | wc -l`;; *compressed*) PART1=`gunzip -c $0 | head -n 1000 | wc -l`;; *empty*) PART1=0;; esac;", "if [[ $0 && ! $1 ]]; then", "SALMON_CMD+=\"-r $0\";", "if [[ $PART1 -lt 1000 ]]; then", ">&2 printf \"Not enough reads to run Salmon: fq: %s\" \"$((PART1/4))\"; exit 0; fi;", "elif [[ $0 && $1 ]]; then", "SALMON_CMD+=\"-1 $0 -2 $1\";", - "case `file $1` in *ASCII*) PART2=`head -c 50K $1 | wc -l`;; *compressed*) PART2=`gunzip -c $1 | head -c 50K | wc -l`;; *empty*) PART2=0;; esac;", + "case `file $1` in *ASCII*) PART2=`head -n 1000 $1 | wc -l`;; *compressed*) PART2=`gunzip -c $1 | head -n 1000 | wc -l`;; *empty*) PART2=0;; esac;", "if [[ $PART1 -lt 1000 || $PART2 -lt 1000 ]]; then", ">&2 printf \"Not enough reads to run Salmon: fq1: %s - fq2: %s\" \"$((PART1/4))\" \"$((PART2/4))\"; exit 0; fi; fi;", "$SALMON_CMD'", From 8d7ef7eab75569980ae27b11ba47cfe8576a4e2e Mon Sep 17 00:00:00 2001 From: Steven Leonard Date: Mon, 11 Feb 2019 11:04:51 +0000 Subject: [PATCH 2/3] added missing arg in check --- data/vtlib/salmon_alignment.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/vtlib/salmon_alignment.json b/data/vtlib/salmon_alignment.json index 92dca6b1e..968784fa9 100644 --- a/data/vtlib/salmon_alignment.json +++ b/data/vtlib/salmon_alignment.json @@ -99,7 +99,7 @@ "--geneMap", {"subst":"annotation_val", "required":"yes"}, "--output", {"subst":"salmon_out"}, {"subst":"b2c_mt", "ifnull":{"subst_constructor":{ "vals":[ "-p", {"subst":"b2c_mt_val"} ]}}}, "\";", - "case `file $0` in *ASCII*) PART1=`head -n 1000 | wc -l`;; *compressed*) PART1=`gunzip -c $0 | head -n 1000 | wc -l`;; *empty*) PART1=0;; esac;", + "case `file $0` in *ASCII*) PART1=`head -n 1000 $0 | wc -l`;; *compressed*) PART1=`gunzip -c $0 | head -n 1000 | wc -l`;; *empty*) PART1=0;; esac;", "if [[ $0 && ! $1 ]]; then", "SALMON_CMD+=\"-r $0\";", "if [[ $PART1 -lt 1000 ]]; then", From dbf218a5526836e425c444a46255e2bbeefe9db4 Mon Sep 17 00:00:00 2001 From: mgcam Date: Thu, 14 Feb 2019 11:42:00 +0000 Subject: [PATCH 3/3] updated Changes file for release 0.24.1 --- Changes | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Changes b/Changes index 0cc499bf0..20e7e9797 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,7 @@ CHANGES LOG ----------- +release 0.24.1 + - correct count of minimum reads to run Salmon release 0.24.0 - allow format selection for stage1 outputs/stage2 inputs (default: cram)