From 3d2e6bffa3a938b7e40aa43d62136da9988d154c Mon Sep 17 00:00:00 2001 From: Luca Beltrame Date: Tue, 9 Dec 2025 10:54:24 +0100 Subject: [PATCH 1/4] Bump ichorCNA package build in ichorcna/createpon and ichorcna/run At the moment, creating a PoN without data on chromosome X is bound to fail due to a bug in ichorCNA(https://github.com/GavinHaLab/ichorCNA/pull/26). It is unclear when a new version will be out, so I have patched the current bioconda package (https://github.com/bioconda/bioconda-recipes/pull/61045) and built new container images, which I want to update to in this PR. --- modules/nf-core/ichorcna/createpon/environment.yml | 2 +- modules/nf-core/ichorcna/createpon/main.nf | 4 ++-- modules/nf-core/ichorcna/run/environment.yml | 2 +- modules/nf-core/ichorcna/run/main.nf | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/ichorcna/createpon/environment.yml b/modules/nf-core/ichorcna/createpon/environment.yml index 54df91b4f29..5073fc57792 100644 --- a/modules/nf-core/ichorcna/createpon/environment.yml +++ b/modules/nf-core/ichorcna/createpon/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::r-ichorcna=0.5.1 + - bioconda::r-ichorcna=0.5.1=r44hdfd78af_1 diff --git a/modules/nf-core/ichorcna/createpon/main.nf b/modules/nf-core/ichorcna/createpon/main.nf index ab19a0332c2..3be817e0c2c 100644 --- a/modules/nf-core/ichorcna/createpon/main.nf +++ b/modules/nf-core/ichorcna/createpon/main.nf @@ -3,8 +3,8 @@ process ICHORCNA_CREATEPON { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.5.1--r43hdfd78af_0' : - 'biocontainers/r-ichorcna:0.5.1--r43hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f07cec06705b4443052d3d7eaccebdbd0078366f7d074bfd4a6893980c6e2c4b/data' : + 'community.wave.seqera.io/library/r-ichorcna:0.5.1--eed4be826f05c9d4' }" input: path wigs diff --git a/modules/nf-core/ichorcna/run/environment.yml b/modules/nf-core/ichorcna/run/environment.yml index 54df91b4f29..5073fc57792 100644 --- a/modules/nf-core/ichorcna/run/environment.yml +++ b/modules/nf-core/ichorcna/run/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::r-ichorcna=0.5.1 + - bioconda::r-ichorcna=0.5.1=r44hdfd78af_1 diff --git a/modules/nf-core/ichorcna/run/main.nf b/modules/nf-core/ichorcna/run/main.nf index 68cf302fc1b..f8fd2eea3a2 100644 --- a/modules/nf-core/ichorcna/run/main.nf +++ b/modules/nf-core/ichorcna/run/main.nf @@ -4,8 +4,8 @@ process ICHORCNA_RUN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.5.1--r43hdfd78af_0' : - 'biocontainers/r-ichorcna:0.5.1--r43hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f07cec06705b4443052d3d7eaccebdbd0078366f7d074bfd4a6893980c6e2c4b/data' : + 'community.wave.seqera.io/library/r-ichorcna:0.5.1--eed4be826f05c9d4' }" input: tuple val(meta), path(wig) From 73e2c18f8109857a44012c95f148023838addf93 Mon Sep 17 00:00:00 2001 From: Luca Beltrame Date: Tue, 9 Dec 2025 11:31:19 +0100 Subject: [PATCH 2/4] Update some md5sums --- modules/nf-core/ichorcna/createpon/tests/main.nf.test.snap | 2 +- modules/nf-core/ichorcna/run/tests/main.nf.test.snap | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/ichorcna/createpon/tests/main.nf.test.snap b/modules/nf-core/ichorcna/createpon/tests/main.nf.test.snap index fe73d2efe9a..3be0d107b23 100644 --- a/modules/nf-core/ichorcna/createpon/tests/main.nf.test.snap +++ b/modules/nf-core/ichorcna/createpon/tests/main.nf.test.snap @@ -18,7 +18,7 @@ "PoN.rds", "PoN.txt", [ - "versions.yml:md5,59dbc83520b9e00a736f49ed2513657a" + "versions.yml:md5,4a4f8b452427ec9438cf0ffad62c7a7d" ] ], "meta": { diff --git a/modules/nf-core/ichorcna/run/tests/main.nf.test.snap b/modules/nf-core/ichorcna/run/tests/main.nf.test.snap index 7a70f7bd51d..1cd749f40e5 100644 --- a/modules/nf-core/ichorcna/run/tests/main.nf.test.snap +++ b/modules/nf-core/ichorcna/run/tests/main.nf.test.snap @@ -134,7 +134,7 @@ ] ], "versions": [ - "versions.yml:md5,d2d30cedd49c7bffdcb74313e8a074c4" + "versions.yml:md5,0395d992ef3e4aa41ed95603f461cc92" ] } ], @@ -147,7 +147,7 @@ "no_panel": { "content": [ [ - "versions.yml:md5,d2d30cedd49c7bffdcb74313e8a074c4" + "versions.yml:md5,0395d992ef3e4aa41ed95603f461cc92" ], "test_genomeWide.pdf", "test.RData", From 8ff90eec4770d5908ea27f5eb4433ef018c306a4 Mon Sep 17 00:00:00 2001 From: Luca Beltrame Date: Tue, 9 Dec 2025 11:33:41 +0100 Subject: [PATCH 3/4] Update test snapshot --- modules/nf-core/ichorcna/run/tests/main.nf.test.snap | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/ichorcna/run/tests/main.nf.test.snap b/modules/nf-core/ichorcna/run/tests/main.nf.test.snap index 1cd749f40e5..13e21009b58 100644 --- a/modules/nf-core/ichorcna/run/tests/main.nf.test.snap +++ b/modules/nf-core/ichorcna/run/tests/main.nf.test.snap @@ -67,7 +67,7 @@ ] ], "8": [ - "versions.yml:md5,d2d30cedd49c7bffdcb74313e8a074c4" + "versions.yml:md5,0395d992ef3e4aa41ed95603f461cc92" ], "cna_seg": [ [ @@ -139,10 +139,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-08-02T06:38:13.140234725" + "timestamp": "2025-12-09T11:32:23.125027221" }, "no_panel": { "content": [ From 222b813430379afa5823983fb28c668aac13fa66 Mon Sep 17 00:00:00 2001 From: Luca Beltrame Date: Tue, 9 Dec 2025 11:36:36 +0100 Subject: [PATCH 4/4] Update test snapshot --- .../ichorcna/createpon/tests/main.nf.test.snap | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/ichorcna/createpon/tests/main.nf.test.snap b/modules/nf-core/ichorcna/createpon/tests/main.nf.test.snap index 3be0d107b23..4a2615ab045 100644 --- a/modules/nf-core/ichorcna/createpon/tests/main.nf.test.snap +++ b/modules/nf-core/ichorcna/createpon/tests/main.nf.test.snap @@ -4,14 +4,14 @@ "PoN_median.rds", "PoN_median.txt", [ - "versions.yml:md5,59dbc83520b9e00a736f49ed2513657a" + "versions.yml:md5,4a4f8b452427ec9438cf0ffad62c7a7d" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-08-06T14:23:09.884294332" + "timestamp": "2025-12-09T11:34:25.04737792" }, "stub": { "content": [ @@ -32,13 +32,13 @@ "PoN_median.rds", "PoN_median.txt", [ - "versions.yml:md5,59dbc83520b9e00a736f49ed2513657a" + "versions.yml:md5,4a4f8b452427ec9438cf0ffad62c7a7d" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-08-06T14:23:29.496424481" + "timestamp": "2025-12-09T11:34:34.559159568" } } \ No newline at end of file