clinical-genomics-lund / nexomeflow

NextFlow pipeline for Exome samples

NexomeFlow a NextFlow pipeline adapted for singularity and slurm execution on HOPPER cluster in Lund

Concept

nexomeflow's Issues

nextflow.config

Move everything that is currently hardcoded to nextflow.config and create one such file for each environment.

add indel cadds failure

create tmpdir, cp file...
Done!
pull out all indels from vcf and collect them in separate file...
Done!
start score.sh on all ins/dels from XXXX-XX.marksplice.vcf.indels...
/opt/bin/add_missing_CADDs_1.4.sh: line 36: /data/bnf/sw/cadd/1.4/CADD-scripts/CADD_2.sh: No such file or directory

Picard syntax

Picard seems to finally transition to a saner command line syntax. This should be fixed everywhere Picard is called in the pipeline.

* NOTE: Picard's command line syntax is changing.
*
* For more information, please see:
* https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
*
* The command line looks like this in the new syntax:
*
*    CollectHsMetrics -I XXXX-XX.markdup.bam -O XXXX-XX.markdup.bam.hsmetrics -R /fs1/resources/ref/hg19/fasta/human_g1k_v37_decoy.fasta -BAIT_INTERVALS /fs1/resources/ref/hg19/bed/agilent_clinical_research_exome_v2/S30409818_Regions.nochr.bed.interval_list -TARGET_INTERVALS /fs1/resources/ref/hg19/bed/agilent_clinical_research_exome_v2/S30409818_Regions.nochr.bed.interval_list
*

Hard coded path to script

The split_normalize process has hardcoded path to local directory: /data/bnf/scripts/exome_DPAF_filter.pl

Add to container?

R missing in container

Picard CollectInsertSizeMetrics requires Rscript, but R appears to not be included in the container.