Added more complete a long example about running a workflow with a pre-determined set of parameters

Author: jmfernandez

sample-work-to-measure/download-and-run-nextflow-workflow.bash

@@ -0,0 +1,99 @@
+#!/bin/bash
+
+workdir="$(mktemp -d --tmpdir treecript_demo_nextflow.XXXXXXXXXX)"
+#workdir=/tmp/ATINA/WORKDIR
+#mkdir -p "$workdir"
+
+cleanup() {
+	set +e
+	# This is needed in order to avoid
+	# potential "permission denied" messages
+	chmod -R u+w "${workdir}"
+	rm -rf "${workdir}"
+}
+
+trap cleanup EXIT
+
+downloadDir="${workdir}/downloads"
+mkdir -p "${downloadDir}"
+
+jvm=https://github.com/AdoptOpenJDK/openjdk11-upstream-binaries/releases/download/jdk-11.0.16%2B8/OpenJDK11U-jdk-shenandoah_x64_linux_11.0.16_8.tar.gz
+#nextflow=https://github.com/nextflow-io/nextflow/releases/download/v24.04.0/nextflow-24.04.0-all
+nextflow=https://github.com/nextflow-io/nextflow/releases/download/v19.04.1/nextflow-19.04.1-all
+workflow=https://github.com/inab/Wetlab2Variations/archive/31348ed533961f84cf348bf1af660ad9de6f870c.zip
+
+declare -a general_rawreads=(
+	ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/140407_D00360_0017_BH947YADXX/Project_RM8398/Sample_U5c/U5c_CCGTCC_L001_R1_001.fastq.gz
+	ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/140407_D00360_0017_BH947YADXX/Project_RM8398/Sample_U5c/U5c_CCGTCC_L001_R2_001.fastq.gz
+)
+
+declare general_referencegenome=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
+
+declare -a BSQR_files=(
+	ftp://ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz
+	ftp://ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz
+)
+
+declare -a BSQR_indexes=(
+	ftp://ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz
+	ftp://ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.idx.gz
+)
+
+bwamem_rgheader='@RG\tID:H947YADXX\tSM:NA12878\tPL:ILLUMINA'
+
+echo Fetching jvm, nextflow and workflow
+wget -c -nv -P "${downloadDir}" "${jvm}" "${nextflow}" "${workflow}"
+
+echo Sleeping 2 seconds
+sleep 2
+
+echo Fetching input files
+wget -c -nv -P "${downloadDir}" "${general_rawreads[@]}" "${general_referencegenome}"
+wget -c -nv -P "${downloadDir}" --user=gsapubftp-anonymous --password=  "${BSQR_files[@]}" "${BSQR_indexes[@]}"
+
+echo Sleeping 2 more seconds
+sleep 2
+
+softDir="${workdir}/soft"
+
+if [ ! -d "${softDir}" ] ; then
+	mkdir -p "${softDir}"
+
+	echo Install JVM
+	tar -x -C "${softDir}" -f "${downloadDir}"/OpenJDK*
+	mv "${softDir}"/openjdk-*/* "${softDir}"
+
+	echo Install Nextflow
+	cp -p "${downloadDir}"/nextflow* "${softDir}"/bin/nextflow
+	chmod +x "${softDir}"/bin/nextflow*
+
+	echo Extract workflow
+	unzip -d "${workdir}" "${downloadDir}"/*.zip
+fi
+
+JAVA_HOME="${softDir}"
+export JAVA_HOME
+PATH="${softDir}/bin:$PATH"
+export PATH
+
+echo Creating yaml run file
+cat > "${workdir}"/input_params.yml <<EOF
+general:
+  rawreads:
+    - ${downloadDir}/U5c_CCGTCC_L001_R1_001.fastq.gz
+    - ${downloadDir}/U5c_CCGTCC_L001_R2_001.fastq.gz
+  referencegenome: ${downloadDir}/hs37d5.fa.gz
+BSQR:
+  files:
+    - ${downloadDir}/Mills_and_1000G_gold_standard.indels.b37.vcf.gz
+    - ${downloadDir}/dbsnp_138.b37.vcf.gz
+  indexes:
+    - ${downloadDir}/Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz
+    - ${downloadDir}/dbsnp_138.b37.vcf.idx.gz
+bwamem:
+  rgheader: '${bwamem_rgheader}'
+outputDir: ${workdir}/OUTPUTS
+metricsDir: ${workdir}/WFMETRICS
+EOF
+
+nextflow run "${workdir}"/Wetlab2Variations-*/nextflow -params-file "${workdir}"/input_params.yml