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Merge pull request mriffle#17 from ajmaurais/pdc
Add PDC as an input file source
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,75 @@ | ||
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| def format_client_args(var) { | ||
| ret = (var == null ? "" : var) | ||
| return ret | ||
| } | ||
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| process GET_STUDY_METADATA { | ||
| publishDir "${params.result_dir}/pdc", failOnError: true, mode: 'copy' | ||
| errorStrategy 'retry' | ||
| maxRetries 5 | ||
| label 'process_low_constant' | ||
| container params.images.pdc_client | ||
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| input: | ||
| val pdc_study_id | ||
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| output: | ||
| path('study_metadata.tsv'), emit: metadata | ||
| path('study_metadata_annotations.csv'), emit: skyline_annotations | ||
| env(study_id), emit: study_id | ||
| env(study_name), emit: study_name | ||
| path('pdc_client_version.txt'), emit: version | ||
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| shell: | ||
| n_files_arg = params.pdc.n_raw_files == null ? "" : "--nFiles ${params.pdc.n_raw_files}" | ||
| pdc_client_args = params.pdc.client_args == null ? "" : params.pdc.client_args | ||
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| ''' | ||
| study_id=$(PDC_client studyID !{pdc_client_args} !{pdc_study_id} | tee study_id.txt) | ||
| study_name=$(PDC_client studyName --normalize !{pdc_client_args} ${study_id} | tee study_name.txt) | ||
| PDC_client metadata !{pdc_client_args} -f tsv !{n_files_arg} --skylineAnnotations ${study_id} | ||
| echo "pdc_client_git_repo='$GIT_REPO - $GIT_BRANCH [$GIT_SHORT_HASH]'" > pdc_client_version.txt | ||
| ''' | ||
| } | ||
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| process METADATA_TO_SKY_ANNOTATIONS { | ||
| label 'process_low_constant' | ||
| container params.images.pdc_client | ||
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| input: | ||
| path pdc_study_metadata | ||
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| output: | ||
| path('skyline_annotations.csv'), emit: skyline_annotations | ||
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| shell: | ||
| ''' | ||
| PDC_client metadataToSky !{pdc_study_metadata} | ||
| ''' | ||
| } | ||
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| process GET_FILE { | ||
| storeDir "${params.panorama_cache_directory}" | ||
| label 'process_low_constant' | ||
| container params.images.pdc_client | ||
| errorStrategy 'retry' | ||
| maxRetries 1 | ||
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| input: | ||
| tuple val(url), val(file_name), val(md5) | ||
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| output: | ||
| path(file_name), emit: downloaded_file | ||
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| shell: | ||
| ''' | ||
| PDC_client file -o '!{file_name}' -m '!{md5}' '!{url}' | ||
| ''' | ||
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| stub: | ||
| """ | ||
| touch ${file_name} | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
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| include { GET_STUDY_METADATA } from "../modules/pdc.nf" | ||
| include { METADATA_TO_SKY_ANNOTATIONS } from "../modules/pdc.nf" | ||
| include { GET_FILE } from "../modules/pdc.nf" | ||
| include { MSCONVERT } from "../modules/msconvert.nf" | ||
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| workflow get_pdc_study_metadata { | ||
| emit: | ||
| study_name | ||
| metadata | ||
| annotations_csv | ||
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| main: | ||
| if(params.pdc.metadata_tsv == null) { | ||
| GET_STUDY_METADATA(params.pdc.study_id) | ||
| metadata = GET_STUDY_METADATA.out.metadata | ||
| annotations_csv = GET_STUDY_METADATA.out.skyline_annotations | ||
| study_name = GET_STUDY_METADATA.out.study_name | ||
| } else { | ||
| metadata = Channel.fromPath(file(params.pdc.metadata_tsv, checkIfExists: true)) | ||
| METADATA_TO_SKY_ANNOTATIONS(metadata) | ||
| annotations_csv = METADATA_TO_SKY_ANNOTATIONS.out | ||
| study_name = params.pdc.study_name | ||
| } | ||
| } | ||
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| workflow get_pdc_files { | ||
| emit: | ||
| study_name | ||
| metadata | ||
| annotations_csv | ||
| wide_mzml_ch | ||
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| main: | ||
| get_pdc_study_metadata() | ||
| metadata = get_pdc_study_metadata.out.metadata | ||
| annotations_csv = get_pdc_study_metadata.out.annotations_csv | ||
| study_name = get_pdc_study_metadata.out.study_name | ||
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| metadata \ | ||
| | splitCsv(header:true, sep:'\t') \ | ||
| | map{row -> tuple(row.url, row.file_name, row.md5sum)} \ | ||
| | GET_FILE | ||
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| MSCONVERT(GET_FILE.out.downloaded_file, | ||
| params.msconvert.do_demultiplex, | ||
| params.msconvert.do_simasspectra) | ||
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| wide_mzml_ch = MSCONVERT.out.mzml_file | ||
| } | ||
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