From be41d00dc0ee4670666b752453b2499694ecdfb8 Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Thu, 11 Mar 2021 22:49:16 -0600 Subject: [PATCH] Finish update seqwho process to match updated version --- rna-seq.nf | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/rna-seq.nf b/rna-seq.nf index 0d19c5a..c047b31 100644 --- a/rna-seq.nf +++ b/rna-seq.nf @@ -857,9 +857,9 @@ process seqwho { gzip sampled.1.seed300.fastq & wait seqwho.py -f sampled.1.seed*.fastq.gz -x SeqWho.ix - seqtypeR1_1=\$(cat SeqWho_call.tsv | grep sampled.1.seed100.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ") - seqtypeR1_2=\$(cat SeqWho_call.tsv | grep sampled.1.seed200.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ") - seqtypeR1_3=\$(cat SeqWho_call.tsv | grep sampled.1.seed300.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ") + seqtypeR1_1=\$(cat SeqWho_call.tsv | grep sampled.1.seed100.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ") + seqtypeR1_2=\$(cat SeqWho_call.tsv | grep sampled.1.seed200.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ") + seqtypeR1_3=\$(cat SeqWho_call.tsv | grep sampled.1.seed300.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ") cp SeqWho_call.tsv SeqWho_call_sampledR1.tsv if [ "\${seqtypeR1_1}" == "\${seqtypeR1}" ] && [ "\${seqtypeR1_2}" == "\${seqtypeR1}" ] && [ "\${seqtypeR1_3}" == "\${seqtypeR1}" ] then @@ -878,9 +878,9 @@ process seqwho { gzip sampled.2.seed300.fastq & wait seqwho.py -f sampled.2.seed*.fastq.gz -x SeqWho.ix - seqtypeR2_1=\$(cat SeqWho_call.tsv | grep sampled.2.seed100.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ") - seqtypeR2_2=\$(cat SeqWho_call.tsv | grep sampled.2.seed200.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ") - seqtypeR2_3=\$(cat SeqWho_call.tsv | grep sampled.2.seed300.fastq.gz | cut -f18 -d\$'\t' | cut -f2 -d":" | tr -d " ") + seqtypeR2_1=\$(cat SeqWho_call.tsv | grep sampled.2.seed100.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ") + seqtypeR2_2=\$(cat SeqWho_call.tsv | grep sampled.2.seed200.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ") + seqtypeR2_3=\$(cat SeqWho_call.tsv | grep sampled.2.seed300.fastq.gz | cut -f19 -d\$'\t' | cut -f2 -d":" | tr -d " ") cp SeqWho_call.tsv SeqWho_call_sampledR2.tsv if [ "\${seqtypeR2_1}" == "\${seqtypeR1}" ] && [ "\${seqtypeR2_2}" == "\${seqtypeR1}" ] && [ "\${seqtypeR2_3}" == "\${seqtypeR1}" ] then -- GitLab