chipseq.py -c $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/chipseq/chipseq.beluga.ini -r readsets.chipseq.txt -d design.chipseq.txt > chipseqCommands.sh

rnaseq.py -c $MUGQIC_PIPELINES_HOME/pipelines/rnaseq/rnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/rnaseq/rnaseq.beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt > rnaseqCommands.sh

dnaseq.py -t mugqic -c $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.beluga.ini -r readset.dnaseq.txt > dnaseqCommands_mugqic.sh

dnaseq.py -t mpileup -c $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.beluga.ini -r readset.dnaseq.txt > dnaseqCommands_mpileup.sh

dnaseq_high_coverage.py -c $MUGQIC_PIPELINES_HOME/pipelines/dnaseq_high_coverage/dnaseq_high_coverage.base.ini $MUGQIC_PIPELINES_HOME/pipelines/dnaseq_high_coverage/dnaseq_high_coverage.beluga.ini -r readset.dnaseq.txt > dnaseq_high_coverageCommands.sh

tumor_pair.py -c $MUGQIC_PIPELINES_HOME/pipelines/dnaseq/dnaseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/tumor_pair/tumor_pair.base.ini $MUGQIC_PIPELINES_HOME/pipelines/tumor_pair/tumor_pair.beluga.ini -r readset.tumorPair.txt -p pairs.csv > tumor_pairCommands.sh

hicseq.py -c $MUGQIC_PIPELINES_HOME/pipelines/hicseq/hicseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/hicseq/hicseq.beluga.ini -r readsets.hicseq.txt -t hic -e MboI > hicseqCommands_hic.sh

hicseq.py -c $MUGQIC_PIPELINES_HOME/pipelines/hicseq/hicseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/hicseq/hicseq.beluga.ini $TEST_DIR/testdata/hicseq/capture.ini -r readsets.HiC010.tsv -t capture -e DpnII > hicseqCommands_capture.sh

rnaseq_light.py -c $MUGQIC_PIPELINES_HOME/pipelines/rnaseq_light/rnaseq_light.base.ini $MUGQIC_PIPELINES_HOME/pipelines/rnaseq_light/rnaseq_light.beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt > rnaseqLightCommands.sh

rnaseq_denovo_assembly.py -c $MUGQIC_PIPELINES_HOME/pipelines/rnaseq_denovo_assembly/rnaseq_denovo_assembly.base.ini $MUGQIC_PIPELINES_HOME/pipelines/rnaseq_denovo_assembly/rnaseq_denovo_assembly.beluga.ini -r readset.rnaseq.txt -d design.rnaseq.txt > rnaseqDeNovoCommands.sh

methylseq.py -c $MUGQIC_PIPELINES_HOME/pipelines/methylseq/methylseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/methylseq/methylseq.beluga.ini -r readset.methylseq.txt > methylseq.sh

pacbio_assembly.py -c $MUGQIC_PIPELINES_HOME/pipelines/pacbio_assembly/pacbio_assembly.base.ini $MUGQIC_PIPELINES_HOME/pipelines/pacbio_assembly/pacbio_assembly.beluga.ini -r readset.pacbio.txt > pacbioCommands.sh

ampliconseq.py -c $MUGQIC_PIPELINES_HOME/pipelines/ampliconseq/ampliconseq.base.ini $MUGQIC_PIPELINES_HOME/pipelines/ampliconseq/ampliconseq.beluga.ini -r readset.ampliconseq.txt > ampliconseqCommands.sh