From fbc70eb4ead5f20ffa6c1050ecf6ee12dcd8f303 Mon Sep 17 00:00:00 2001 From: Elena Buscaroli Date: Fri, 19 Sep 2025 17:50:47 +0200 Subject: [PATCH 1/6] fixing minor bug --- modules/nf-core/mobster/templates/main_script.R | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/mobster/templates/main_script.R b/modules/nf-core/mobster/templates/main_script.R index f0fa9b5b5f4d..a688f50aaf9e 100644 --- a/modules/nf-core/mobster/templates/main_script.R +++ b/modules/nf-core/mobster/templates/main_script.R @@ -65,6 +65,7 @@ run_mobster_fit = function(joint_table, descr) { # remove mutations with VAF < min_VAF inp_tb = joint_table %>% + dplyr::filter(VAF < 1) %>% dplyr::mutate(adj_VAF=VAF/!!purity) %>% dplyr::filter(adj_VAF>=as.numeric(opt[["min_VAF"]])) %>% dplyr::filter(karyotype=="1:1") %>% From 7890bdcce79d82837ce6e6b547e94f1f21ec55d6 Mon Sep 17 00:00:00 2001 From: Elena Buscaroli Date: Wed, 21 Jan 2026 12:06:50 +0100 Subject: [PATCH 2/6] updating tool version --- modules/nf-core/mobster/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/mobster/environment.yml b/modules/nf-core/mobster/environment.yml index cb9434645327..ee990ebf5cb7 100644 --- a/modules/nf-core/mobster/environment.yml +++ b/modules/nf-core/mobster/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge - bioconda dependencies: -- bioconda::r-cnaqc=1.1.2 +- bioconda::r-cnaqc=1.1.3 - bioconda::r-mobster=0.1.1 - conda-forge::r-cli=3.6.5 - conda-forge::r-dplyr=1.1.4 From abeedf69c989e882ebff790a3cdb363aa4d432fa Mon Sep 17 00:00:00 2001 From: Elena Buscaroli Date: Wed, 21 Jan 2026 12:07:08 +0100 Subject: [PATCH 3/6] updating docker and singularity containers --- modules/nf-core/mobster/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/mobster/main.nf b/modules/nf-core/mobster/main.nf index 4a7b30ab7500..c8a45d3398e7 100644 --- a/modules/nf-core/mobster/main.nf +++ b/modules/nf-core/mobster/main.nf @@ -4,8 +4,8 @@ process MOBSTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/de/de31ce602ca40639c817dcd0f99f0260719a9a5f269759791d03576491ea3e87/data': - 'community.wave.seqera.io/library/r-cnaqc_r-mobster_r-cli_r-dplyr_r-ggplot2:96c0dbada588b39a' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c9/c9ef4992af6754a36358a4fc7a52bdc3928c012070f06140a44ddcf174da4e62/data': + 'community.wave.seqera.io/library/r-cnaqc_r-mobster_r-cli_r-dplyr_r-ggplot2:5a94f700b38065ea' }" input: tuple val(meta), path(rds_join) From f794f41cff1e2853149be0d589651d073472202b Mon Sep 17 00:00:00 2001 From: Elena Buscaroli Date: Wed, 21 Jan 2026 12:07:18 +0100 Subject: [PATCH 4/6] setting run in parallel as FALSE --- modules/nf-core/mobster/templates/main_script.R | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/mobster/templates/main_script.R b/modules/nf-core/mobster/templates/main_script.R index a688f50aaf9e..4db37bae68bd 100644 --- a/modules/nf-core/mobster/templates/main_script.R +++ b/modules/nf-core/mobster/templates/main_script.R @@ -76,6 +76,7 @@ run_mobster_fit = function(joint_table, descr) { tail = eval(parse(text=opt[["tail"]])), pi_cutoff = as.numeric(opt[["pi_cutoff"]]), N_cutoff = as.integer(opt[["n_cutoff"]]), + parallel = FALSE, description = descr) } From 7955da13efe62d816a28b8494a1639a7255c46cf Mon Sep 17 00:00:00 2001 From: Elena Buscaroli Date: Wed, 21 Jan 2026 15:31:11 +0100 Subject: [PATCH 5/6] Update main.nf.test.snap --- .../nf-core/mobster/tests/main.nf.test.snap | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/modules/nf-core/mobster/tests/main.nf.test.snap b/modules/nf-core/mobster/tests/main.nf.test.snap index a41717285bc9..559fb1943315 100644 --- a/modules/nf-core/mobster/tests/main.nf.test.snap +++ b/modules/nf-core/mobster/tests/main.nf.test.snap @@ -2,26 +2,26 @@ "test rds input": { "content": [ [ - "versions.yml:md5,233827868ca632b6611b69337aa5de2b" + "versions.yml:md5,33352102a5ea4278214d90ca36bb4425" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.10.2" }, - "timestamp": "2025-07-21T18:19:29.811857" + "timestamp": "2026-01-21T15:14:16.168458" }, "test csv input": { "content": [ [ - "versions.yml:md5,233827868ca632b6611b69337aa5de2b" + "versions.yml:md5,33352102a5ea4278214d90ca36bb4425" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.10.2" }, - "timestamp": "2025-07-21T18:23:21.783643" + "timestamp": "2026-01-21T15:18:45.141969" }, "test csv input - stub": { "content": [ @@ -87,7 +87,7 @@ ] ], "6": [ - "versions.yml:md5,75c7b43f6746354f65b3534ce8949372" + "versions.yml:md5,af4bfdb43f7b9a49e026f4508be7ea96" ], "mobster_best_plots_rds": [ [ @@ -150,15 +150,15 @@ ] ], "versions": [ - "versions.yml:md5,75c7b43f6746354f65b3534ce8949372" + "versions.yml:md5,af4bfdb43f7b9a49e026f4508be7ea96" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-09-17T13:03:15.343446" + "timestamp": "2026-01-21T15:20:46.541349" }, "test rds input - stub": { "content": [ @@ -224,7 +224,7 @@ ] ], "6": [ - "versions.yml:md5,75c7b43f6746354f65b3534ce8949372" + "versions.yml:md5,af4bfdb43f7b9a49e026f4508be7ea96" ], "mobster_best_plots_rds": [ [ @@ -287,14 +287,14 @@ ] ], "versions": [ - "versions.yml:md5,75c7b43f6746354f65b3534ce8949372" + "versions.yml:md5,af4bfdb43f7b9a49e026f4508be7ea96" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nextflow": "25.10.2" }, - "timestamp": "2025-09-17T12:59:01.526617" + "timestamp": "2026-01-21T15:16:09.445968" } } \ No newline at end of file From 6ddcc6583a87ff51ea877d1ca7cae21a915eefd7 Mon Sep 17 00:00:00 2001 From: Elena Buscaroli Date: Wed, 21 Jan 2026 15:31:19 +0100 Subject: [PATCH 6/6] prettier --- modules/nf-core/mobster/environment.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/mobster/environment.yml b/modules/nf-core/mobster/environment.yml index 31d4fcf3640a..7044a59c7ccd 100644 --- a/modules/nf-core/mobster/environment.yml +++ b/modules/nf-core/mobster/environment.yml @@ -2,8 +2,8 @@ channels: - conda-forge - bioconda dependencies: -- bioconda::r-cnaqc=1.1.3 -- bioconda::r-mobster=0.1.1 -- conda-forge::r-cli=3.6.5 -- conda-forge::r-dplyr=1.1.4 -- conda-forge::r-ggplot2=3.5.2 \ No newline at end of file + - bioconda::r-cnaqc=1.1.3 + - bioconda::r-mobster=0.1.1 + - conda-forge::r-cli=3.6.5 + - conda-forge::r-dplyr=1.1.4 + - conda-forge::r-ggplot2=3.5.2