From 4c5c8034ab1689679b2cba2b2e1c34e298ea779d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 18 Sep 2023 09:32:02 +0200
Subject: [PATCH] add line number check for subsample and split
---
.gitignore | 7 +++++++
src/modules/sample_reads.nf | 12 ++++++++++--
src/modules/split.nf | 3 +++
3 files changed, 20 insertions(+), 2 deletions(-)
diff --git a/.gitignore b/.gitignore
index d88c0bc..b03679d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,10 @@ src/mergekmer
.Rhistory
.Rprofile
.kmer-diff.Rproj
+.Rbuildignore
+doc/2023_09_18_presentation.html
+doc/2023_09_18_presentation_files/
+doc/presentation_files/
+fail.txt
+kmer-diff.Rproj
+src/plot_counts.Rmd
diff --git a/src/modules/sample_reads.nf b/src/modules/sample_reads.nf
index 6bce0b3..e10d4ec 100644
--- a/src/modules/sample_reads.nf
+++ b/src/modules/sample_reads.nf
@@ -120,10 +120,18 @@ process SAMPLE_READS {
error "SEQTK/SAMPLE must have a sample_size value included"
}
"""
- if [\$(cat $sample_size | tr -d '\\n') -eq \$(cat $read_number | tr -d '\\n')]; then
+ SAMPLE_SIZE=\$((cat $sample_size | tr -d '\\n'))
+ CURRENT_READ_NUMBER=\$((cat $read_number | tr -d '\\n'))
+
+ if [\$SAMPLE_SIZE -eq \$CURRENT_READ_NUMBER]; then
ln -s ${reads} sample_${reads}
+ READ_NUMBER=\$((cat $sample_size | tr -d '\\n'))
else
- zcat ${reads} | head -n \$(cat $sample_size | tr -d '\\n') | gzip -c > sample_${reads}
+ zcat ${reads} | head -n \$((cat $sample_size | tr -d '\\n')) | gzip -c > sample_${reads}
+ READ_NUMBER=\$((zcat sample_${reads} | wc -l))
+ fi
+ if [\$SAMPLE_SIZE -ne \$READ_NUMBER]; then
+ exit 1
fi
cat <<-END_VERSIONS > versions.yml
diff --git a/src/modules/split.nf b/src/modules/split.nf
index a6cf5fe..9a8b72f 100644
--- a/src/modules/split.nf
+++ b/src/modules/split.nf
@@ -16,6 +16,9 @@ process SPLIT {
"""
zcat ${fastq} | split -l 4000000 - ${fastq.simpleName}_
+ ls -l ${fastq.simpleName}_* | \\
+ awk '{system("if [\$((wc -l "\$9")) -ne 4000000]; then exit 1; fi")}'
+
ls -l ${fastq.simpleName}_* | \\
awk '{system("gzip -c "\$9" > "\$9".fastq.gz && rm "\$9)}'
--
GitLab