Examples: Pipeline Launch Commands
ampliconseq
user@machine:~$ genpipes ampliconseq -c $GENPIPES_INIS/ampliconseq/ampliconseq.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.ampliconseq.txt \ -s 1-8 \ -g ampliconseqCommands.sh user@machine:~$ bash ampliconseqCommands.sh
chipseq
user@machine:~$ genpipes chipseq -c $GENPIPES_INIS/chipseq/chipseq.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readsets.chipseq.txt \ -d design.chipseq.txt \ -s 1-19 \ -g chipseqCommands.sh user@machine:~$ bash chipseqCommands.sh
covseq
user@machine:~$ genpipes covseq -c $GENPIPES_INIS/covseq/covseq.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ $GENPIPES_INIS/covseq/ARTIC_v4.1.ini \ -r readset.covseq.txt \ -g covseqCommands_mugqic.sh user@machine:~$ bash covseqCommands_mugqic.sh
nanopore covseq
user@machine:~$ genpipes nanopore_covseq -c $GENPIPES_INIS/nanopore/nanopore.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ $GENPIPES_INIS/nanopore_covseq/ARTIC_v4.1.ini \ -r readset.default.nanopore_covseq.txt -g nanopore_covseq_cmd.sh user@machine:~$ bash nanopore_covseq_cmd
rnaseq
user@machine:~$ genpipes rnaseq -c $GENPIPES_INIS/rnaseq/rnaseq.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.rnaseq.txt \ -d design.rnaseq.txt \ -s 1-21 \ -g rnaseqCommands.sh user@machine:~$ bash rnaseqCommands.sh
dnaseq
user@machine:~$ genpipes dnaseq -t germline_high_cov \ -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini \ $GENPIPES_INIS/dnaseq/dnaseq.high_cov.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.dnaseq.txt \ -s 1-15 \ -g dnaseq_germ_high_cov_cmd.sh user@machine:~$ bash dnaseq_germ_high_cov_cmd.sh
user@machine:~$ genpipes dnaseq -t germline_snv -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.dnaseq.txt \ -s 1-27 \ -j slurm \ -g dnaseq_germline_snv_cmd.sh user@machine:~$ bash dnaseq_germline_snv_cmd.sh
user@machine:~$ genpipes dnaseq -t germline_sv -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini \ $GENPIPES_INIS/dnaseq/dnaseq.sv.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.dnaseq.txt \ -s 1-25 \ -g dnaseq_germ_sv_cmd.sh user@machine:~$ bash dnaseq_germ_sv_cmd.sh
user@machine:~$ genpipes dnaseq -t somatic_ensemble \ -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini \ $GENPIPES_INIS/dnaseq/dnaseq.cancer.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.somatic_ensemble.txt \ -p pairs.somatic_ensemble.csv \ -s 1-38 \ -j slurm \ -g dnaseq_somatic_ensemble_cmd.sh user@machine:~$ bash dnaseq_somatic_ensemble_cmd.sh
user@machine:~$ genpipes dnaseq -t somatic_fastpass \ -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini \ $GENPIPES_INIS/dnaseq/dnaseq.cancer.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.somatic_fastpass.txt \ -p pairs.somatic_fastpass.csv \ -s 1-38 \ -j slurm \ -g dnaseq_somatic_fastpass_cmd.sh user@machine:~$ bash dnaseq_somatic_fastpass_cmd.sh
user@machine:~$ genpipes dnaseq -t somatic_sv \ -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini \ $GENPIPES_INIS/dnaseq/dnaseq.cancer.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.somatic_sv.txt \ -p pairs.somatic_sv.csv \ -s 1-38 \ -j slurm \ -g dnaseq_somatic_sv_cmd.sh user@machine:~$ bash dnaseq_somatic_sv_cmd.sh
user@machine:~$ genpipes dnaseq -t somatic_tumor_only \ -c $GENPIPES_INIS/dnaseq/dnaseq.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.somatic_tumor_only.txt \ -s 1-38 \ -j slurm \ -g dnaseq_somatic_tumor_cmd.sh user@machine:~$ bash dnaseq_somatic_tumor_cmd.sh
rnaseq_light
user@machine:~$ genpipes rnaseq_light -c $GENPIPES_INIS/rnaseq_light/rnaseq_light.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.rnaseq.txt \ -d design.rnaseq.txt \ -s 1-8 \ -g rnaseq_light_cmd.sh user@machine:~$ bash rnaseq_light_cmd.sh
rnaseq_denovo_assembly
user@machine:~$ genpipes rnaseq_denovo_assembly -c $GENPIPES_INIS/rnaseq_denovo_assembly/rnaseq_denovo_assembly.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.rnaseq.txt -d design.rnaseq.txt \ -s 1-24 \ -g rnaseq_denovo_cmd.sh user@machine:~$ bash rnaseq_denovo_cmd.sh
methylseq
user@machine:~$ genpipes methylseq -c $GENPIPES_INIS/methylseq/methylseq.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r readset.methylseq.txt \ -s 1-15,17-18 \ -g methylseq.sh user@machine:~$ bash methylseq.sh
longread
user@machine:~$ genpipes longread_dnaseq -t nanopore \ -c $GENPIPES_INIS/longread/longread.base.ini $GENPIPES_INIS/common_ini/rorqual.ini \ -r /cvmfs/soft.mugqic/root/testdata/nanopore/readset.nanopore.txt \ -o nanopore \ -g longread_nanopore_cmd.sh user@machine:~$ bash longread_nanopore_cmd.sh
user@machine:~$ genpipes longread_dnaseq -t revio \ -c $GENPIPES_INIS/longread/longread.base.ini \ $GENPIPES_INIS/common_ini/rorqual.ini \ -r /cvmfs/soft.mugqic/root/testdata/longread_dnaseq/readset.revio.txt \ -o revio \ -g longread_revio_cmd.sh user@machine:~$ bash longread_revio_cmd.sh
Tip
Depending upon the cluster where you are executing the pipeline, substitute the file name rorqual.ini in the command with the appropriate <DRAC server cluster name>.ini file located in the $GENPIPES_INIS/common_ini folder.
For e.g., rorqual.ini, fir.ini, or narval.ini.