fix: add missing bai to exomedepth, fix typo in start script

start_marple_marvin.sh

@@ -41,6 +41,6 @@ snakemake --profile /projects/wp3/nobackup/TwistCancer/Bin/marple_rd_tc/profiles
 
 ## Cp Results to OUTBOX and trigger stackstorm
 echo 'Pipeline done, cp back data and trigger stackstorm' && \
-rsync -ru /scratch/wp3/TwistCancer/${sequencerun}/Results/ ${outbox}/${sequencerun}/ && \
-touch ${outbox}/${sequencerun}/Done.txt && \
+rsync -ru /scratch/wp3/TwistCancer/${sequenceid}/Results/ ${outbox}/${sequenceid}/ && \
+touch ${outbox}/${sequenceid}/Done.txt && \
 echo 'All done!'

workflow/Snakefile

@@ -74,6 +74,7 @@ use rule * from cnv_sv as cnv_sv_*
 use rule exomedepth_call from cnv_sv as cnv_sv_exomedepth_call with:
     input:
         bam="alignment/samtools_merge_bam/{sample}_{type}.bam",
+        bai="alignment/samtools_merge_bam/{sample}_{type}.bam.bai",
         bedfile=config.get("exomedepth_call", {}).get("bedfile", ""),
         ref_count=config["exomedepth_call"]["ref_count"],
         genes=config.get("exomedepth_call", {}).get("genesfile", ""),