Fix path for ControlFREEC

[FedericoComoglio]

Hi everyone,

running sarek v2.5 with ControlFREEC among the tools, returned

[0;35m[nf-core/sarek] Pipeline completed with errors
Error executing process > 'ControlFreecViz (T_vs_N)'

Caused by:
  Process `ControlFreecViz (T_vs_N)` terminated with an error exit status (1)

Command executed:

  cat /opt/conda/envs/sarek-2.5/bin/assess_significance.R | R --slave --args T.pileup.gz_CNVs T.pileup.gz_ratio.txt
  cat /opt/conda/envs/sarek-2.5/bin/assess_significance.R | R --slave --args T.pileup.gz_normal_CNVs T.pileup.gz_normal_ratio.txt
  cat /opt/conda/envs/sarek-2.5/bin/makeGraph.R | R --slave --args 2 T.pileup.gz_ratio.txt T.pileup.gz_BAF.txt
  cat /opt/conda/envs/sarek-2.5/bin/makeGraph.R | R --slave --args 2 T.pileup.gz_normal_ratio.txt N.pileup.gz_BAF.txt
  perl /opt/conda/envs/sarek-2.5/bin/freec2bed.pl -f T.pileup.gz_ratio.txt > T.bed
  perl /opt/conda/envs/sarek-2.5/bin/freec2bed.pl -f T.pileup.gz_normal_ratio.txt > N.bed

Command exit status:
  1

Command output:
  (empty)

Command error:
  cat: /opt/conda/envs/sarek-2.5/bin/assess_significance.R: No such file or directory

The reason is that /opt/conda/envs/sarek-2.5/bin/assess_significance.R is actually /opt/conda/envs/nf-core-sarek-2.5/bin/assess_significance.R

A quick check suggests to fix the path in:

grep 'envs/sarek-' main.nf
    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvTumor} ${ratioTumor}
    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvNormal} ${ratioNormal}
    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioTumor} ${bafTumor}
    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioNormal} ${bafNormal}
    perl /opt/conda/envs/sarek-${workflow.manifest.version}/bin/freec2bed.pl -f ${ratioTumor} > ${idSampleTumor}.bed
    perl /opt/conda/envs/sarek-${workflow.manifest.version}/bin/freec2bed.pl -f ${ratioNormal} > ${idSampleNormal}.bed
    genesplicer = params.genesplicer ? "--plugin GeneSplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/bin/genesplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/share/genesplicer-1.0-1/human,context=200,tmpdir=\$PWD/${reducedVCF}" : "--offline"
    genesplicer = params.genesplicer ? "--plugin GeneSplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/bin/genesplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/share/genesplicer-1.0-1/human,context=200,tmpdir=\$PWD/${reducedVCF}" : "--offline"

The run completed successfully after fixing this.

Federico