Merge pull request #90 from icgc-argo/argo-data-submission-wf@1.0.3

[release]
icgc-argo · Jul 21, 2023 · 13c8ae4 · 13c8ae4
2 parents 341adba + dab9679
commit 13c8ae4
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Showing 12 changed files with 12 additions and 12 deletions.
diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf
@@ -22,7 +22,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '1.0.2'
+version = '1.0.3'
 
 // universal params go here, change default value as needed
 params.container = ""
@@ -165,7 +165,7 @@ submissionReceipt_params = [
 ]
 
 include { SongScoreUpload as uploadWf } from './wfpr_modules/github.com/icgc-argo-workflows/nextflow-data-processing-utility-tools/song-score-upload@2.9.3/main.nf' params(upload_params)
-include { validateSeqtools as valSeq} from './wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8/main.nf' params(validateSeq_params)
+include { validateSeqtools as valSeq} from './wfpr_modules/github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.9/main.nf' params(validateSeq_params)
 include { EgaDownloadWf as egaWf } from './wfpr_modules/github.com/icgc-argo/argo-data-submission/ega-download-wf@0.1.6/main.nf' params(egaDownload_params)
 include { payloadGenSeqExperiment as pGenExp} from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3/main.nf' params(payloadGen_params)
 include { cleanupWorkdir as cleanup } from './wfpr_modules/github.com/icgc-argo-workflows/data-processing-utility-tools/cleanup-workdir@1.0.0.1/main.nf'

diff --git a/argo-data-submission-wf/pkg.json b/argo-data-submission-wf/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "argo-data-submission-wf",
-    "version": "1.0.2",
+    "version": "1.0.3",
     "description": "ARGO data submission workflow",
     "main": "main.nf",
     "deprecated": false,
@@ -12,7 +12,7 @@
         "url": "https://github.com/icgc-argo/argo-data-submission.git"
     },
     "dependencies": [
-        "github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8",
+        "github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.9",
         "github.com/icgc-argo/argo-data-submission/ega-download-wf@0.1.6",
         "github.com/icgc-argo-workflows/data-processing-utility-tools/payload-gen-seq-experiment@0.8.3",
         "github.com/icgc-argo-workflows/data-processing-utility-tools/cleanup-workdir@1.0.0.1",

diff --git a/argo-data-submission-wf/tests/checker.nf b/argo-data-submission-wf/tests/checker.nf
@@ -26,7 +26,7 @@
 */
 
 nextflow.enable.dsl = 2
-version = '1.0.2'
+version = '1.0.3'
 
 // universal params
 params.publish_dir = ""

diff --git a/argo-data-submission-wf/tests/input/read_group_local.tsv b/argo-data-submission-wf/tests/input/read_group_local.tsv
@@ -1,5 +1,5 @@
 type	submitter_read_group_id	read_group_id_in_bam	submitter_sequencing_experiment_id	platform_unit	is_paired_end	file_r1	file_r2	read_length_r1	read_length_r2	insert_size	sample_barcode	library_name
-read_group	QCMG_866d65b8-ff3f-11e4-b413-bdbd66be296d_130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA.1_8043985	QCMG:866d65b8-ff3f-11e4-b413-bdbd66be296d:130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA.1	EXP-9	QCMG_866d65b8-ff3f-11e4-b413-bdbd66be296d_130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA.1_8043985	true	anon_chr1_complete.bam	anon_chr1_complete.bam	101	101			RNA-Seq:QCMG:QCMG:130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA:RNA-Seq:QCMG:Illumina TruSeq for Library_20130620_F
-read_group	QCMG_91ce15f2-ff3e-11e4-9d73-85b485b025f8_130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA.1_8043985	QCMG:91ce15f2-ff3e-11e4-9d73-85b485b025f8:130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA.1	EXP-9	QCMG_91ce15f2-ff3e-11e4-9d73-85b485b025f8_130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA.1_8043985	true	anon_chr1_complete.bam	anon_chr1_complete.bam	101	101			RNA-Seq:QCMG:QCMG:130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA:RNA-Seq:QCMG:Illumina TruSeq for Library_20130620_F
-read_group	QCMG_dd3f83b8-ff3e-11e4-81af-910d0943bdb6_130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA.1_8043985	QCMG:dd3f83b8-ff3e-11e4-81af-910d0943bdb6:130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA.1	EXP-9	QCMG_dd3f83b8-ff3e-11e4-81af-910d0943bdb6_130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA.1_8043985	true	anon_chr1_complete.bam	anon_chr1_complete.bam	101	101			RNA-Seq:QCMG:QCMG:130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA:RNA-Seq:QCMG:Illumina TruSeq for Library_20130620_F
-read_group	QCMG_22f321c6-ff3f-11e4-8e8b-f8a0800c69f0_130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA.1_8043985	QCMG:22f321c6-ff3f-11e4-8e8b-f8a0800c69f0:130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA.1	EXP-9	QCMG_22f321c6-ff3f-11e4-8e8b-f8a0800c69f0_130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA.1_8043985	true	anon_chr1_complete.bam	anon_chr1_complete.bam	101	101			RNA-Seq:QCMG:QCMG:130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA:RNA-Seq:QCMG:Illumina TruSeq for Library_20130620_F
+read_group	QCMG_866d65b8-ff3f-11e4-b413-bdbd66be296d_130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA.1_8043985	QCMG:866d65b8-ff3f-11e4-b413-bdbd66be296d:130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA.1	EXP-9	QCMG_866d65b8-ff3f-11e4-b413-bdbd66be296d_130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA.1_8043985	true	anon_chr1_complete.bam	anon_chr1_complete.bam	101	101			RNA-Seq:QCMG:QCMG:130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA:RNA-Seq:QCMG:20130620_F
+read_group	QCMG_91ce15f2-ff3e-11e4-9d73-85b485b025f8_130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA.1_8043985	QCMG:91ce15f2-ff3e-11e4-9d73-85b485b025f8:130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA.1	EXP-9	QCMG_91ce15f2-ff3e-11e4-9d73-85b485b025f8_130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA.1_8043985	true	anon_chr1_complete.bam	anon_chr1_complete.bam	101	101			RNA-Seq:QCMG:QCMG:130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA:RNA-Seq:QCMG:20130620_F
+read_group	QCMG_dd3f83b8-ff3e-11e4-81af-910d0943bdb6_130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA.1_8043985	QCMG:dd3f83b8-ff3e-11e4-81af-910d0943bdb6:130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA.1	EXP-9	QCMG_dd3f83b8-ff3e-11e4-81af-910d0943bdb6_130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA.1_8043985	true	anon_chr1_complete.bam	anon_chr1_complete.bam	101	101			RNA-Seq:QCMG:QCMG:130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA:RNA-Seq:QCMG:20130620_F
+read_group	QCMG_22f321c6-ff3f-11e4-8e8b-f8a0800c69f0_130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA.1_8043985	QCMG:22f321c6-ff3f-11e4-8e8b-f8a0800c69f0:130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA.1	EXP-9	QCMG_22f321c6-ff3f-11e4-8e8b-f8a0800c69f0_130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA.1_8043985	true	anon_chr1_complete.bam	anon_chr1_complete.bam	101	101			RNA-Seq:QCMG:QCMG:130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA:RNA-Seq:QCMG:20130620_F
diff --git a/...ion/validate-seqtools@0.1.8/.dockerignore → ...ion/validate-seqtools@0.1.9/.dockerignore b/...ion/validate-seqtools@0.1.8/.dockerignore → ...ion/validate-seqtools@0.1.9/.dockerignore
diff --git a/...ission/validate-seqtools@0.1.8/Dockerfile → ...ission/validate-seqtools@0.1.9/Dockerfile b/...ission/validate-seqtools@0.1.8/Dockerfile → ...ission/validate-seqtools@0.1.9/Dockerfile
@@ -37,7 +37,7 @@ RUN cd /tmp &&\
 
 # Install seq-tools
 
-RUN pip install git+https://github.com/icgc-argo/seq-tools.git@1.2.5
+RUN pip install git+https://github.com/icgc-argo/seq-tools.git@1.2.6
 #RUN git clone https://github.com/icgc-argo/seq-tools.git@1.1.0 &&\
 #    git clone https://github.com/icgc-argo/seq-tools.git@1.1.0
 #    cd seq-tools &&\

diff --git a/...mission/validate-seqtools@0.1.8/README.md → ...mission/validate-seqtools@0.1.9/README.md b/...mission/validate-seqtools@0.1.8/README.md → ...mission/validate-seqtools@0.1.9/README.md
diff --git a/...ubmission/validate-seqtools@0.1.8/main.nf → ...ubmission/validate-seqtools@0.1.9/main.nf b/...ubmission/validate-seqtools@0.1.8/main.nf → ...ubmission/validate-seqtools@0.1.9/main.nf
@@ -25,7 +25,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.8'
+version = '0.1.9'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.validate-seqtools'

diff --git a/...ubmission/validate-seqtools@0.1.8/main.py → ...ubmission/validate-seqtools@0.1.9/main.py b/...ubmission/validate-seqtools@0.1.8/main.py → ...ubmission/validate-seqtools@0.1.9/main.py
diff --git a/...n/validate-seqtools@0.1.8/nextflow.config → ...n/validate-seqtools@0.1.9/nextflow.config b/...n/validate-seqtools@0.1.8/nextflow.config → ...n/validate-seqtools@0.1.9/nextflow.config
diff --git a/...bmission/validate-seqtools@0.1.8/pkg.json → ...bmission/validate-seqtools@0.1.9/pkg.json b/...bmission/validate-seqtools@0.1.8/pkg.json → ...bmission/validate-seqtools@0.1.9/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "validate-seqtools",
-    "version": "0.1.8",
+    "version": "0.1.9",
     "description": "Using Seq-tools, validates molecular",
     "main": "main.nf",
     "deprecated": false,

diff --git a/...sion/validate-seqtools@0.1.8/wfpr_modules → ...sion/validate-seqtools@0.1.9/wfpr_modules b/...sion/validate-seqtools@0.1.8/wfpr_modules → ...sion/validate-seqtools@0.1.9/wfpr_modules