Merge pull request #44 from icgc-argo/schema-update

Schema update
icgc-argo-workflows · Apr 17, 2020 · 82ce31d · 82ce31d
2 parents 016a3cc + 14fcd7a
commit 82ce31d
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Showing 11 changed files with 15 additions and 15 deletions.
diff --git a/dna-seq-alignment/main.nf b/dna-seq-alignment/main.nf
@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 nextflow.preview.dsl = 2
 name = 'dna-seq-alignment'
-version = '1.0.6'
+version = '1.1.0-dev'
 
 /*
 ========================================================================================
@@ -183,8 +183,8 @@ include {bwaMemAligner; getBwaSecondaryFiles} from "./modules/raw.githubusercont
 include readGroupUBamQC as rgQC from "./modules/raw.githubusercontent.com/icgc-argo/data-qc-tools-and-wfs/read-group-ubam-qc.0.1.2.0/tools/read-group-ubam-qc/read-group-ubam-qc.nf" params(readGroupUBamQC_params)
 include {bamMergeSortMarkdup as merSorMkdup; getMdupSecondaryFile} from "./modules/raw.githubusercontent.com/icgc-argo/dna-seq-processing-tools/bam-merge-sort-markdup.0.1.10.0/tools/bam-merge-sort-markdup/bam-merge-sort-markdup.nf" params(bamMergeSortMarkdup_params)
 include {alignedSeqQC; getAlignedQCSecondaryFiles} from "./modules/raw.githubusercontent.com/icgc-argo/data-qc-tools-and-wfs/aligned-seq-qc.0.2.2.0/tools/aligned-seq-qc/aligned-seq-qc" params(alignedSeqQC_params)
-include payloadGenDnaAlignment as pGenDnaAln from "./modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-dna-alignment.0.1.6.1/tools/payload-gen-dna-alignment/payload-gen-dna-alignment.nf" params(payloadGenDnaAlignment_params)
-include payloadGenDnaSeqQc as pGenDnaSeqQc from "./modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-dna-seq-qc.0.2.4.1/tools/payload-gen-dna-seq-qc/payload-gen-dna-seq-qc.nf" params(payloadGenDnaSeqQc_params)
+include payloadGenDnaAlignment as pGenDnaAln from "./modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-dna-alignment.0.2.0.0/tools/payload-gen-dna-alignment/payload-gen-dna-alignment.nf" params(payloadGenDnaAlignment_params)
+include payloadGenDnaSeqQc as pGenDnaSeqQc from "./modules/raw.githubusercontent.com/icgc-argo/data-processing-utility-tools/payload-gen-dna-seq-qc.0.3.0.0/tools/payload-gen-dna-seq-qc/payload-gen-dna-seq-qc.nf" params(payloadGenDnaSeqQc_params)
 include {gatkSplitIntervals as splitItvls; getSecondaryFiles as getSIIdx} from "./modules/raw.githubusercontent.com/icgc-argo/gatk-tools/gatk-split-intervals.4.1.4.1-1.0/tools/gatk-split-intervals/gatk-split-intervals"
 include {gatkCollectOxogMetrics as oxog; getOxogSecondaryFiles; gatherOxogMetrics as gatherOM} from "./modules/raw.githubusercontent.com/icgc-argo/gatk-tools/gatk-collect-oxog-metrics.4.1.4.1-1.5/tools/gatk-collect-oxog-metrics/gatk-collect-oxog-metrics" params(gatkCollectOxogMetrics_params)
 include songScoreUpload as upAln from './song-score-utils/song-score-upload' params(uploadAlignment_params)

diff --git a/...na-alignment/payload-gen-dna-alignment.nf → ...na-alignment/payload-gen-dna-alignment.nf b/...na-alignment/payload-gen-dna-alignment.nf → ...na-alignment/payload-gen-dna-alignment.nf
@@ -24,7 +24,7 @@
  */
 
 nextflow.preview.dsl=2
-version = '0.1.6.1'
+version = '0.2.0.0'
 
 params.files_to_upload = ""
 params.seq_experiment_analysis = ""

diff --git a/...-gen-dna-seq-qc/payload-gen-dna-seq-qc.nf → ...-gen-dna-seq-qc/payload-gen-dna-seq-qc.nf b/...-gen-dna-seq-qc/payload-gen-dna-seq-qc.nf → ...-gen-dna-seq-qc/payload-gen-dna-seq-qc.nf
@@ -23,7 +23,7 @@
  */
 
 nextflow.preview.dsl=2
-version = '0.2.4.1'
+version = '0.3.0.0'
 
 params.seq_experiment_analysis = ""
 params.qc_files = []

diff --git a/...ity-tools/1.1.2/process/score_download.nf → ...ity-tools/1.1.3/process/score_download.nf b/...ity-tools/1.1.2/process/score_download.nf → ...ity-tools/1.1.3/process/score_download.nf
@@ -6,7 +6,7 @@ params.cpus = 8
 params.mem = 20
 
 // required params w/ default
-params.container_version = '3.1.1'
+params.container_version = '5.0.0'
 params.transport_mem = 2 // Transport memory is in number of GBs
 
 // required params, no default

diff --git a/...ility-tools/1.1.2/process/score_upload.nf → ...ility-tools/1.1.3/process/score_upload.nf b/...ility-tools/1.1.2/process/score_upload.nf → ...ility-tools/1.1.3/process/score_upload.nf
@@ -6,7 +6,7 @@ params.cpus = 8
 params.mem = 20
 
 // required params w/ default
-params.container_version = '3.1.1'
+params.container_version = '5.0.0'
 params.transport_mem = 2 // Transport memory is in number of GBs
 
 // required params, no default

diff --git a/...-tools/1.1.2/process/song_get_analysis.nf → ...-tools/1.1.3/process/song_get_analysis.nf b/...-tools/1.1.2/process/song_get_analysis.nf → ...-tools/1.1.3/process/song_get_analysis.nf
diff --git a/...lity-tools/1.1.2/process/song_manifest.nf → ...lity-tools/1.1.3/process/song_manifest.nf b/...lity-tools/1.1.2/process/song_manifest.nf → ...lity-tools/1.1.3/process/song_manifest.nf
diff --git a/...ility-tools/1.1.2/process/song_publish.nf → ...ility-tools/1.1.3/process/song_publish.nf b/...ility-tools/1.1.2/process/song_publish.nf → ...ility-tools/1.1.3/process/song_publish.nf
diff --git a/...tility-tools/1.1.2/process/song_submit.nf → ...tility-tools/1.1.3/process/song_submit.nf b/...tility-tools/1.1.2/process/song_submit.nf → ...tility-tools/1.1.3/process/song_submit.nf
diff --git a/song-score-utils/song-score-download.nf b/song-score-utils/song-score-download.nf
@@ -12,7 +12,7 @@ params.score_api_token = ''
 
 // required params w/ default
 params.song_container_version = '4.2.0'
-params.score_container_version = '3.1.1'
+params.score_container_version = '5.0.0'
 
 // required params, no default
 // --song_url         song url for download process (defaults to main song_url param)
@@ -38,8 +38,8 @@ score_params = [
 
 // import modules
 // TODO: change import for score_download after it's updated on the other git repo
-include songGetAnalysis as songGet from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.2/process/song_get_analysis' params(song_params)
-include scoreDownload as scoreDn from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.2/process/score_download' params(score_params)
+include songGetAnalysis as songGet from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.3/process/song_get_analysis' params(song_params)
+include scoreDownload as scoreDn from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.3/process/score_download' params(score_params)
 
 workflow songScoreDownload {
     take:

diff --git a/song-score-utils/song-score-upload.nf b/song-score-utils/song-score-upload.nf
@@ -14,7 +14,7 @@ params.extract_mem = 1
 
 // required params w/ default
 params.song_container_version = '4.2.0'
-params.score_container_version = '3.1.1'
+params.score_container_version = '5.0.0'
 params.extract_container_version = 'latest'
 
 // required params, no default
@@ -47,10 +47,10 @@ extract_params = [
 
 // import modules
 // TODO: change import for song_manifest after it's updated (use non-root docker image) on the other git repo
-include songSubmit as songSub from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.2/process/song_submit' params(song_params)
-include songManifest as songMan from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.2/process/song_manifest' params(song_params)
-include scoreUpload as scoreUp from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.2/process/score_upload' params(score_params)
-include songPublish as songPub from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.2/process/song_publish' params(song_params)
+include songSubmit as songSub from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.3/process/song_submit' params(song_params)
+include songManifest as songMan from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.3/process/song_manifest' params(song_params)
+include scoreUpload as scoreUp from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.3/process/score_upload' params(score_params)
+include songPublish as songPub from '../modules/raw.githubusercontent.com/icgc-argo/nextflow-data-processing-utility-tools/1.1.3/process/song_publish' params(song_params)
 
 workflow songScoreUpload {
     take: