1.2.0

Please see the following document for a full breakdown.

Whats changed:

• updated clinical URLs from collaboratory to cumulus
• fixed code for handling JSON payloads

Utilizes the following packages:
argo-data-submission-wf.v1.2.0
validate-seqtools.v0.1.9
ega-download-wf.v0.1.6
download-aspera@0.1.3
download-pyega3@0.2.0
decrypt-aspera@0.1.1
sanity-check.v0.1.3
payload-gen-seq-experiment@0.8.3
cleanup-workdir@1.0.0.1
cram2bam@0.1.0
payload-json-to-tsvs@0.1.2
submission-receipt@0.1.0
song-score-upload@2.9.3

argo-data-submission-wf.v1.2.0

• Release argo-data-submission-wf.v1.2.0 (5c5a3d1)
• Package argo-data-submission-wf.v1.2.0.tar.gz (sha256: 2f45130ec325692f788fa0cb6830c5bcbd885f9d53f9dea4c4f547be523fcda0)
• Package URI github.com/icgc-argo/argo-data-submission/argo-data-submission-wf@1.2.0
• Run the package: nextflow run icgc-argo/argo-data-submission/argo-data-submission-wf/main.nf -r argo-data-submission-wf.v1.2.0 -params-file <params-json-file>

1.1.0

Please see the following document for a full breakdown.

Whats changed:

• updated song and score URLs from collaboratory to cumulus
• updated score-client version to 5.10.0
• added --skip_upload true flag to run a noncommittal run
• added profile checks

Utilizes the following packages:
argo-data-submission-wf.v1.1.0
validate-seqtools.v0.1.9
ega-download-wf.v0.1.6
download-aspera@0.1.3
download-pyega3@0.2.0
decrypt-aspera@0.1.1
sanity-check.v0.1.3
payload-gen-seq-experiment@0.8.3
cleanup-workdir@1.0.0.1
cram2bam@0.1.0
payload-json-to-tsvs@0.1.2
submission-receipt@0.1.0
song-score-upload@2.9.3

argo-data-submission-wf.v1.1.0

• Release argo-data-submission-wf.v1.1.0 (30bb5d3)
• Package argo-data-submission-wf.v1.1.0.tar.gz (sha256: 8990906154fb90f9dbc356c4e5591f2db9eb9c1b5d9266e1c2cb806b4e07888a)
• Package URI github.com/icgc-argo/argo-data-submission/argo-data-submission-wf@1.1.0
• Run the package: nextflow run icgc-argo/argo-data-submission/argo-data-submission-wf/main.nf -r argo-data-submission-wf.v1.1.0 -params-file <params-json-file>

1.0.3

Please see the following document for a full breakdown.

Whats changed:

• added new flag for seq-tools to skip "SM" in bam header check

Utilizes the following packages:
argo-data-submission-wf.v1.0.3
validate-seqtools.v0.1.9
ega-download-wf.v0.1.6
download-aspera@0.1.3
download-pyega3@0.2.0
decrypt-aspera@0.1.1
sanity-check.v0.1.3
payload-gen-seq-experiment@0.8.3
cleanup-workdir@1.0.0.1
cram2bam@0.1.0
payload-json-to-tsvs@0.1.2
submission-receipt@0.1.0
song-score-upload@2.9.3

argo-data-submission-wf.v1.0.3

• Release argo-data-submission-wf.v1.0.3 (13c8ae4)
• Package argo-data-submission-wf.v1.0.3.tar.gz (sha256: 250bd4a8b115ee71d4da83cef04d4fb5226a8df7e0ff0295bd950fdd3987bd63)
• Package URI github.com/icgc-argo/argo-data-submission/argo-data-submission-wf@1.0.3
• Run the package: nextflow run icgc-argo/argo-data-submission/argo-data-submission-wf/main.nf -r argo-data-submission-wf.v1.0.3 -params-file <params-json-file>

validate-seqtools.v0.1.9

• Release validate-seqtools.v0.1.9 (341adba)
• Package validate-seqtools.v0.1.9.tar.gz (sha256: 86d153a5fa8638e8051087836dd4db88ac8f7e139d38a9f7b6756fc1bfcacb92)
• Package URI github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.9
• Run the package: nextflow run icgc-argo/argo-data-submission/validate-seqtools/main.nf -r validate-seqtools.v0.1.9 -params-file <params-json-file>

1.0.2

Please see the following document for a full breakdown.

Whats changed:

• added support for Target-Seq in validate-seqtools and sanity-check
• Added parallelism support for download-pyega3 and validate-seqtools

Utilizes the following packages:
argo-data-submission-wf.v1.0.2
validate-seqtools.v0.1.8
ega-download-wf.v0.1.6
download-aspera@0.1.3
download-pyega3@0.2.0
decrypt-aspera@0.1.1
sanity-check.v0.1.3
payload-gen-seq-experiment@0.8.3
cleanup-workdir@1.0.0.1
cram2bam@0.1.0
payload-json-to-tsvs@0.1.2
submission-receipt@0.1.0
song-score-upload@2.9.3

validate-seqtools.v0.1.8

• Release validate-seqtools.v0.1.8 (88dab3e)
• Package validate-seqtools.v0.1.8.tar.gz (sha256: 6303731737d85ec9dc255b5a6dbaa83c84b023d2393788b95f9e97b60b1f10e3)
• Package URI github.com/icgc-argo/argo-data-submission/validate-seqtools@0.1.8
• Run the package: nextflow run icgc-argo/argo-data-submission/validate-seqtools/main.nf -r validate-seqtools.v0.1.8 -params-file <params-json-file>

sanity-check.v0.1.3

• Release sanity-check.v0.1.3 (a910ea9)
• Package sanity-check.v0.1.3.tar.gz (sha256: 15526432e2923e8e4c9beadefb2e696b8f08ba258077477b7d6cc1eeb5c67ae4)
• Package URI github.com/icgc-argo/argo-data-submission/sanity-check@0.1.3
• Run the package: nextflow run icgc-argo/argo-data-submission/sanity-check/main.nf -r sanity-check.v0.1.3 -params-file <params-json-file>