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Merged
kelly-sovacool merged 5 commits into from
Mar 4, 2026
Merged

chore: merge dev into main #352

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8b44c52
ci: bump ccbr/actions to v0.5 with new print versions script (#345)
kelly-sovacool Mar 4, 2026
51b3d23
docs: 🤖 update readme for spac/spac/Dockerfile.v0.9.1 (#350)
github-actions[bot] Mar 4, 2026
c9a9ac9
docs: 🤖 update readme for superFreq/ccbr_superfreq_1.6/Dockerfile.v1 …
github-actions[bot] Mar 4, 2026
b2c8a96
docs: 🤖 update readme for spac/spac/Dockerfile.v2 (#349)
github-actions[bot] Mar 4, 2026
f0945ca
docs: 🤖 update readme for ichorCNA/ccbr_ichorcna_0.3.2/Dockerfile.v1 …
github-actions[bot] Mar 4, 2026
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3 changes: 1 addition & 2 deletions .github/workflows/build-docker-auto.yml
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Expand Up @@ -95,7 +95,7 @@ jobs:
fetch-depth: 0
ref: ${{ github.ref_name }} # branch name of push

- uses: CCBR/actions/build-docker@v0.4
- uses: CCBR/actions/build-docker@v0.5
with:
dockerfile: ${{ matrix.file }}
dockerhub-namespace: nciccbr
Expand All @@ -104,4 +104,3 @@ jobs:
suffix: ${{ env.suffix }}
push: true
github-token: ${{ github.token }}
json-file: "scripts/tool_version_commands.json"
4 changes: 2 additions & 2 deletions .github/workflows/build-docker-manual.yml
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Expand Up @@ -49,7 +49,7 @@ on:
ccbr-actions-version:
description: "The version or branch of ccbr_actions to use (see https://github.com/ccbr/actions)"
required: true
default: "v0.4"
default: "v0.5"

jobs:
build-docker:
Expand All @@ -62,7 +62,7 @@ jobs:
id: checkout
uses: actions/checkout@v4

- uses: CCBR/actions/build-docker@v0.4
- uses: CCBR/actions/build-docker@v0.5
with:
dockerfile: ${{ github.event.inputs.dockerfile }}
dockerhub-namespace: ${{ github.event.inputs.dockerhub-namespace }}
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4 changes: 2 additions & 2 deletions ichorCNA/ccbr_ichorcna_0.3.2/v1.README.md
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@@ -1,9 +1,9 @@
## CCBR/Dockers2 nciccbr/ccbr_ichorcna_0.3.2:v1

Dockerfile source: https://github.com/CCBR/Dockers2/blob/cc565aa0c3677a77a344fb67b79ba6f5b472c8c0/ichorCNA/ccbr_ichorcna_0.3.2/Dockerfile.v1
Dockerfile source: https://github.com/CCBR/Dockers2/blob/0dca6c675fcbbee459105a7ec23e3b43ba29960b/ichorCNA/ccbr_ichorcna_0.3.2/Dockerfile.v1


Built on: 2026-03-02_17:48:33
Built on: 2026-03-02_18:07:38

Build tag: v1

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143 changes: 0 additions & 143 deletions scripts/tool_version_commands.json
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This file was deleted.

4 changes: 2 additions & 2 deletions spac/spac/v0.9.1.README.md
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@@ -1,9 +1,9 @@
## CCBR/Dockers2 nciccbr/spac:v0.9.1

Dockerfile source: https://github.com/CCBR/Dockers2/blob/cc565aa0c3677a77a344fb67b79ba6f5b472c8c0/spac/spac/Dockerfile.v0.9.1
Dockerfile source: https://github.com/CCBR/Dockers2/blob/0dca6c675fcbbee459105a7ec23e3b43ba29960b/spac/spac/Dockerfile.v0.9.1


Built on: 2026-03-02_17:56:24
Built on: 2026-03-02_18:15:49

Build tag: v0.9.1

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45 changes: 45 additions & 0 deletions spac/spac/v2.README.md
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@@ -0,0 +1,45 @@
## CCBR/Dockers2 nciccbr/spac:v2

Dockerfile source: https://github.com/CCBR/Dockers2/blob/0dca6c675fcbbee459105a7ec23e3b43ba29960b/spac/spac/Dockerfile.v2


Built on: 2026-03-02_18:24:54

Build tag: v2

Base image: continuumio/miniconda3:24.3.0-0

Dockerfile path in repo: spac/spac/Dockerfile.v2


| Tool | Version |
|---------|---------|
| bbtools | NOTINDOCKER |
| bcftools | NOTINDOCKER |
| bedops | NOTINDOCKER |
| bedtools | NOTINDOCKER |
| bowtie | NOTINDOCKER |
| bowtie2 | NOTINDOCKER |
| bwa | NOTINDOCKER |
| cutadapt | NOTINDOCKER |
| fastqc | NOTINDOCKER |
| fastQValidator | NOTINDOCKER |
| fastqscreen | NOTINDOCKER |
| git | 2.30.2 |
| java | NOTINDOCKER |
| kraken2 | NOTINDOCKER |
| kronatools | NOTINDOCKER |
| multiqc | NOTINDOCKER |
| parallel | NOTINDOCKER |
| picard | NOTINDOCKER |
| pigz | NOTINDOCKER |
| preseq | NOTINDOCKER |
| python2 | NOTINDOCKER |
| python3 | 3.9.13 |
| qualimap | NOTINDOCKER |
| rsem | NOTINDOCKER |
| rseqc | NOTINDOCKER |
| samtools | NOTINDOCKER |
| ucsc_tools | NOTINDOCKER |
| vcftools | NOTINDOCKER |

4 changes: 2 additions & 2 deletions superFreq/ccbr_superfreq_1.6/v1.README.md
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@@ -1,9 +1,9 @@
## CCBR/Dockers2 nciccbr/ccbr_superfreq_1.6:v1

Dockerfile source: https://github.com/CCBR/Dockers2/blob/5d77f93f3f7b61cfa5a48319578aacf07d56260d/superFreq/ccbr_superfreq_1.6/Dockerfile.v1
Dockerfile source: https://github.com/CCBR/Dockers2/blob/0dca6c675fcbbee459105a7ec23e3b43ba29960b/superFreq/ccbr_superfreq_1.6/Dockerfile.v1


Built on: 2026-03-02_15:56:54
Built on: 2026-03-02_18:34:50

Build tag: v1

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