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Merged Add multiqc
BIOWDL-135 into develop
Merged Ruben Vorderman requested to merge BIOWDL-135 into develop

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  • Ruben Vorderman
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 6bd11ab2
    • multiqc.wdl
    39 }
    40
    41 String outputDir = if defined(outDir) then select_first([outDir]) else "."
    42
    43 command {
    44 set -e -o pipefail
    45 ~{preCommand}
    46 ~{if defined(outDir) then "mkdir -p " + outputDir else ""}
    47 multiqc \
    48 ~{true="--force" false="" force} \
    49 ~{true="--dirs" false="" dirs} \
    50 ~{"--dirs-depth " + dirsDepth} \
    51 ~{true="--fullnames" false="" fullNames} \
    52 ~{"--title " + title} \
    53 ~{"--comment " + comment} \
    54 ~{"--filename " + fileName} \
  • Ruben Vorderman
  • Ruben Vorderman
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 6bd11ab2
    • multiqc.wdl
    39 }
    40
    41 String outputDir = if defined(outDir) then select_first([outDir]) else "."
    42
    43 command {
    44 set -e -o pipefail
    45 ~{preCommand}
    46 ~{if defined(outDir) then "mkdir -p " + outputDir else ""}
    47 multiqc \
    48 ~{true="--force" false="" force} \
    49 ~{true="--dirs" false="" dirs} \
    50 ~{"--dirs-depth " + dirsDepth} \
    51 ~{true="--fullnames" false="" fullNames} \
    52 ~{"--title " + title} \
    53 ~{"--comment " + comment} \
    54 ~{"--filename " + fileName} \
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 6bd11ab2
    • multiqc.wdl
    39 }
    40
    41 String outputDir = if defined(outDir) then select_first([outDir]) else "."
    42
    43 command {
    44 set -e -o pipefail
    45 ~{preCommand}
    46 ~{if defined(outDir) then "mkdir -p " + outputDir else ""}
    47 multiqc \
    48 ~{true="--force" false="" force} \
    49 ~{true="--dirs" false="" dirs} \
    50 ~{"--dirs-depth " + dirsDepth} \
    51 ~{true="--fullnames" false="" fullNames} \
    52 ~{"--title " + title} \
    53 ~{"--comment " + comment} \
    54 ~{"--filename " + fileName} \
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 6bd11ab2
    • multiqc.wdl
    39 }
    40
    41 String outputDir = if defined(outDir) then select_first([outDir]) else "."
    42
    43 command {
    44 set -e -o pipefail
    45 ~{preCommand}
    46 ~{if defined(outDir) then "mkdir -p " + outputDir else ""}
    47 multiqc \
    48 ~{true="--force" false="" force} \
    49 ~{true="--dirs" false="" dirs} \
    50 ~{"--dirs-depth " + dirsDepth} \
    51 ~{true="--fullnames" false="" fullNames} \
    52 ~{"--title " + title} \
    53 ~{"--comment " + comment} \
    54 ~{"--filename " + fileName} \
    • Ruben Vorderman
      Ruben Vorderman @rhpvorderman ·
      Author Owner

      Multiqc parses this in a complex way. If it ends in html, html is cut off. If it doesn't nothing is cut off. This makes output file name unstable and compensation for that is needed.

  • Ruben Vorderman
  • Ruben Vorderman
    Ruben Vorderman @rhpvorderman started a thread on commit 6bd11ab2
    • multiqc.wdl
    39 }
    40
    41 String outputDir = if defined(outDir) then select_first([outDir]) else "."
    42
    43 command {
    44 set -e -o pipefail
    45 ~{preCommand}
    46 ~{if defined(outDir) then "mkdir -p " + outputDir else ""}
    47 multiqc \
    48 ~{true="--force" false="" force} \
    49 ~{true="--dirs" false="" dirs} \
    50 ~{"--dirs-depth " + dirsDepth} \
    51 ~{true="--fullnames" false="" fullNames} \
    52 ~{"--title " + title} \
    53 ~{"--comment " + comment} \
    54 ~{"--filename " + fileName} \
  • Ruben Vorderman
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