From c441cecdb9b1b17a2782b4b2dd4c61656e471e29 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 12 Oct 2023 16:01:49 +0200
Subject: [PATCH] run.sh: add resume tag
---
run.sh | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
create mode 100644 run.sh
diff --git a/run.sh b/run.sh
new file mode 100644
index 0000000..a6ff9bd
--- /dev/null
+++ b/run.sh
@@ -0,0 +1,33 @@
+cd data/
+# Download the fastq
+awk '{system("fasterq-dump "$0)}' SRR_Acc_List.txt
+ls -l *.fastq \
+ | awk '{system("gzip "$9)}'
+
+# Download the fasta
+aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/ ./GRCh37/
+aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/ ./GRCm38/
+
+# Concatenate the fasta
+
+cat GRCh37/genome.fa \
+ | sed -E 's/(>.*)/\1_GRCh37/g' \
+ > GRCh37_GRCm38_mix.fa
+cat GRCm38/genome.fa \
+ | sed -E 's/(>.*)/\1_GRCm38/g' \
+ >> GRCh37_GRCm38_mix.fa
+
+cd ../
+
+nextflow run main.nf \
+ -profile psmn \
+ --workflow hicpro \
+ --input data/sample.csv \
+ --fasta data/GRCh37_GRCm38_mix.fa \
+ --outdir results/ \
+ --digestion hindiii \
+ --keep_dups \
+ --filter_pcr_picard \
+ -resume
+
+
--
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