From 0173f0a7459a56867cd6042dc8f3b39514fb426a Mon Sep 17 00:00:00 2001 From: Miguel Brown Date: Fri, 16 Jan 2026 16:16:44 -0500 Subject: [PATCH 1/4] :tada: create kf swans docker --- SWANS/v2.1.0/Dockerfile | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 SWANS/v2.1.0/Dockerfile diff --git a/SWANS/v2.1.0/Dockerfile b/SWANS/v2.1.0/Dockerfile new file mode 100644 index 0000000..8bb2cb8 --- /dev/null +++ b/SWANS/v2.1.0/Dockerfile @@ -0,0 +1,9 @@ +ARG PLATFORM=linux/amd64 + +FROM --platform=${PLATFORM} francothyroidlab/pond:1.2 +LABEL maintainer="Miguel Brown " +LABEL description="Single-entity Workflow ANalysiS Pipeline (SWANS)" + +ENV SWANS_VERSION=2.1.0 + +RUN curl -L https://github.com/FrancoResearchLab/SWANS/archive/refs/tags/v${SWANS_VERSION}.tar.gz | tar -xz --wildcards '*/scripts/' --strip-components=3 From dbb0de99423d0cc3432f28fee2531e1d431d5037 Mon Sep 17 00:00:00 2001 From: Miguel Brown Date: Fri, 16 Jan 2026 21:28:08 +0000 Subject: [PATCH 2/4] :pencil: change install dir :plus_sign: add dockerfile --- SWANS/v2.1.0/Dockerfile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/SWANS/v2.1.0/Dockerfile b/SWANS/v2.1.0/Dockerfile index 8bb2cb8..0ab624f 100644 --- a/SWANS/v2.1.0/Dockerfile +++ b/SWANS/v2.1.0/Dockerfile @@ -6,4 +6,8 @@ LABEL description="Single-entity Workflow ANalysiS Pipeline (SWANS)" ENV SWANS_VERSION=2.1.0 +WORKDIR /SWANS + RUN curl -L https://github.com/FrancoResearchLab/SWANS/archive/refs/tags/v${SWANS_VERSION}.tar.gz | tar -xz --wildcards '*/scripts/' --strip-components=3 +WORKDIR / +COPY Dockerfile . \ No newline at end of file From 2cb3953edc8b94ed9fe701eeb1dc7a7de5250694 Mon Sep 17 00:00:00 2001 From: Miguel Brown Date: Tue, 20 Jan 2026 18:08:44 +0000 Subject: [PATCH 3/4] :wrench: fixed image to work with current SWANS NF --- SWANS/v2.1.0/Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/SWANS/v2.1.0/Dockerfile b/SWANS/v2.1.0/Dockerfile index 0ab624f..ee7dcc3 100644 --- a/SWANS/v2.1.0/Dockerfile +++ b/SWANS/v2.1.0/Dockerfile @@ -5,9 +5,11 @@ LABEL maintainer="Miguel Brown " LABEL description="Single-entity Workflow ANalysiS Pipeline (SWANS)" ENV SWANS_VERSION=2.1.0 +ENV PATH="$PATH:/SWANS/src/scripts" + WORKDIR /SWANS -RUN curl -L https://github.com/FrancoResearchLab/SWANS/archive/refs/tags/v${SWANS_VERSION}.tar.gz | tar -xz --wildcards '*/scripts/' --strip-components=3 +RUN curl -L https://github.com/FrancoResearchLab/SWANS/archive/refs/tags/v${SWANS_VERSION}.tar.gz | tar -xz --strip-components=1 WORKDIR / COPY Dockerfile . \ No newline at end of file From d1d22134dcad145e21b8a93a8d0ff0140ab64b6c Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 20 Jan 2026 13:12:46 -0500 Subject: [PATCH 4/4] update docker table (#293) Co-authored-by: migbro --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 4fa2c54..d3b5aef 100644 --- a/README.md +++ b/README.md @@ -176,6 +176,7 @@ supremo|1.0.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/supremo:1.0.0 sv2|latest|docker pull pgc-images.sbgenomics.com/d3b-bixu/sv2:latest svaba|1.1.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/svaba:1.1.0 SVTyper|0.7.1|docker pull pgc-images.sbgenomics.com/d3b-bixu/svtyper:0.7.1 +SWANS|v2.1.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/swans:v2.1.0 t1k|v1.0.2|docker pull pgc-images.sbgenomics.com/d3b-bixu/t1k:v1.0.2 t1k|v1.0.5|docker pull pgc-images.sbgenomics.com/d3b-bixu/t1k:v1.0.5 THetA2|0.7.0|docker pull pgc-images.sbgenomics.com/d3b-bixu/theta2:0.7.0