diff --git a/compress_pipeline.cwl b/compress_pipeline.cwl index 7a1717a06967a38663c1d4f8a2bd1940c3eeed7d..89d734590baee950b4f48b5ad6fa5bf21181bc06 100644 --- a/compress_pipeline.cwl +++ b/compress_pipeline.cwl @@ -25,34 +25,24 @@ outputs: - compress/compressed type: File[] steps: - - id: surl_copy + - id: fetch_data in: - - id: surl + - id: surl_link source: surls - out: - - id: output - run: steps/surl_copy.cwl - label: surl_copy - scatter: - - surl - - id: untar - in: - - id: tar_file - source: surl_copy/output out: - id: uncompressed - run: steps/untar.cwl - label: untar + run: steps/fetch_data.cwl + label: fetch_data scatter: - - tar_file + - surl_link - id: dppp in: - id: parset source: define_parset/output - id: msin - source: untar/uncompressed + source: fetch_data/uncompressed - id: msout_name - source: untar/uncompressed + source: fetch_data/uncompressed valueFrom: '$("COMPRESSED_" + self[0].basename)' - id: writefullresflag default: true @@ -77,7 +67,7 @@ steps: - id: inspect_flagging_dataloss in: - id: input - source: untar/uncompressed + source: fetch_data/uncompressed out: - id: output run: steps/inspect_flagging_dataloss.cwl diff --git a/steps/DPPP.cwl b/steps/DPPP.cwl index 3930e63b6fac35037a204318b009ae41e61060c9..d8a9c604fd0e843fb84a1c952797a03efe17ca50 100755 --- a/steps/DPPP.cwl +++ b/steps/DPPP.cwl @@ -1,7 +1,5 @@ class: CommandLineTool cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' id: dppp baseCommand: - DPPP @@ -91,7 +89,3 @@ stdout: DPPP.log stderr: DPPP_err.log requirements: - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entry: $(inputs.msin) - writable: true diff --git a/steps/untar.cwl b/steps/fetch_data.cwl similarity index 52% rename from steps/untar.cwl rename to steps/fetch_data.cwl index 55d02a9d7e4d3b154312c21c7ef6980d6410ccb8..10e782563ac78537ae3507472bbba602e93d5d3d 100644 --- a/steps/untar.cwl +++ b/steps/fetch_data.cwl @@ -1,10 +1,10 @@ -id: untar -label: untar +id: fetchdata +label: fetch_data class: CommandLineTool cwlVersion: v1.0 inputs: - - id: tar_file - type: File + - id: surl_link + type: string inputBinding: position: 0 @@ -15,16 +15,19 @@ outputs: glob: 'out/*' baseCommand: - 'bash' - - 'untar.sh' + - 'fetch.sh' doc: 'Untar a compressed file' requirements: + InlineJavascriptRequirement: {} InitialWorkDirRequirement: listing: - - entryname: 'untar.sh' + - entryname: 'fetch.sh' entry: | #!/bin/bash mkdir out cd out - tar -xvf $1 + turl=`echo $1 | awk '{gsub("srm://srm.grid.sara.nl[:0-9]*","gsiftp://gridftp.grid.sara.nl"); print}'` + echo "Downloading $turl" + globus-url-copy $turl - | tar -xvf - diff --git a/steps/stage.cwl b/steps/stage.cwl deleted file mode 100644 index 0cc4266af5f67fb477e425d90e9055525473b2e4..0000000000000000000000000000000000000000 --- a/steps/stage.cwl +++ /dev/null @@ -1,21 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' -id: stage -baseCommand: - - gfal-legacy-bringonline -inputs: - - id: input - type: string - inputBinding: - shellQuote: false - position: 0 -outputs: - - id: output - type: string - outputBinding: - outputEval: $(inputs.input) -label: stage -requirements: - - class: InlineJavascriptRequirement diff --git a/steps/surl_copy.cwl b/steps/surl_copy.cwl deleted file mode 100644 index 62223e33c8305957ebac303c3e083737cd70a764..0000000000000000000000000000000000000000 --- a/steps/surl_copy.cwl +++ /dev/null @@ -1,24 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' -id: surl_copy -baseCommand: - - gfal-copy - -inputs: - - id: surl - type: string - inputBinding: - position: -1 -outputs: - - id: output - type: File - outputBinding: - glob: '*' -doc: Download a file give a surl -label: surl_copy -arguments: - - . -temporaryFailCodes: - - 70