run.sh: add resume tag

run.sh

+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
+
+