From eb336d69c3368ea8eb7505bd6d25e82803106bb6 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Wed, 29 Nov 2023 11:19:25 +0100 Subject: [PATCH 1/6] Update samtools in some mulled containers --- combinations/hash.tsv | 3 +++ 1 file changed, 3 insertions(+) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index aafacbfb7..4d91f2a3a 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -499,3 +499,6 @@ r-base=4.3,bioconductor-chipseeker=1.36.0,r-magrittr=2.0.3,bioconductor-genomicf dragmap=1.3.0,samtools=1.18,pigz=2.8 r-base=4.3,r-ggplot2=3.4.4,r-magrittr=2.0.3,r-gridextra=2.3,r-rcolorbrewer=1.1_3,r-data.table=1.14.8 pandas=1.1.4,matchms=0.24.0,click=8.0.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 +cnvkit=0.9.10,samtools=1.18 +gatk4=4.4.0.0,samtools=1.18 +pretextmap=0.1.9,samtools=1.18 From 3521ef86329f141796bf55732f17397c9f9fe91e Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Wed, 29 Nov 2023 11:20:56 +0100 Subject: [PATCH 2/6] Forgot one --- combinations/hash.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 4d91f2a3a..06e05b998 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -502,3 +502,4 @@ pandas=1.1.4,matchms=0.24.0,click=8.0.1 quay.io/bioconda/base-glibc-busybox-bash cnvkit=0.9.10,samtools=1.18 gatk4=4.4.0.0,samtools=1.18 pretextmap=0.1.9,samtools=1.18 +samtools=1.18,ultra_bioinformatics=0.1 From 9cab04a792cdef466c64de73cd88ccc4d114c34d Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Wed, 29 Nov 2023 11:51:06 +0100 Subject: [PATCH 3/6] Added all nf-core mulled containers using samtools --- combinations/hash.tsv | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 06e05b998..a8906b903 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -503,3 +503,20 @@ cnvkit=0.9.10,samtools=1.18 gatk4=4.4.0.0,samtools=1.18 pretextmap=0.1.9,samtools=1.18 samtools=1.18,ultra_bioinformatics=0.1 +bbmap=39.01,samtools=1.18 +biscuit=1.1.0.20220707,samtools=1.18 +bwa=0.7.17,samtools=1.18 +bwa-mem2=2.2.1,samtools=1.18 +chromap=0.2.4,samtools=1.18 +deeptools=3.5.1,samtools=1.18 +hisat2=2.2.1,samtools=1.18 +homer=4.11,samtools=1.18,r-base=4.0.2,bioconductor-deseq2=1.30.0,bioconductor-edger=3.32.0,perl=5.26.2 +manta=1.6.0,samtools=1.18 +minimap2=2.24,samtools=1.18 +qualimap=2.2.2d,samtools=1.18 +samblaster=0.1.26,samtools=1.18 +sequenza-utils=3.0.0,samtools=1.18 +star=2.7.10a,samtools=1.18,gawk=5.1.0 +svdb=2.8.1,samtools=1.18 +vsearch=2.21.1,samtools=1.18 +yara=1.0.2,samtools=1.18 From f7de74641e3a907d56ac1141ef7ff5398662e609 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Wed, 29 Nov 2023 12:36:20 +0100 Subject: [PATCH 4/6] Remove lesser used containers --- combinations/hash.tsv | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index a8906b903..689656d7b 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -501,22 +501,8 @@ r-base=4.3,r-ggplot2=3.4.4,r-magrittr=2.0.3,r-gridextra=2.3,r-rcolorbrewer=1.1_3 pandas=1.1.4,matchms=0.24.0,click=8.0.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 cnvkit=0.9.10,samtools=1.18 gatk4=4.4.0.0,samtools=1.18 -pretextmap=0.1.9,samtools=1.18 -samtools=1.18,ultra_bioinformatics=0.1 -bbmap=39.01,samtools=1.18 -biscuit=1.1.0.20220707,samtools=1.18 bwa=0.7.17,samtools=1.18 bwa-mem2=2.2.1,samtools=1.18 -chromap=0.2.4,samtools=1.18 -deeptools=3.5.1,samtools=1.18 -hisat2=2.2.1,samtools=1.18 -homer=4.11,samtools=1.18,r-base=4.0.2,bioconductor-deseq2=1.30.0,bioconductor-edger=3.32.0,perl=5.26.2 manta=1.6.0,samtools=1.18 minimap2=2.24,samtools=1.18 -qualimap=2.2.2d,samtools=1.18 -samblaster=0.1.26,samtools=1.18 -sequenza-utils=3.0.0,samtools=1.18 star=2.7.10a,samtools=1.18,gawk=5.1.0 -svdb=2.8.1,samtools=1.18 -vsearch=2.21.1,samtools=1.18 -yara=1.0.2,samtools=1.18 From f04f4282642a8764b56fb7c3f32c40cbbbc416c7 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Wed, 29 Nov 2023 12:40:00 +0100 Subject: [PATCH 5/6] split PR --- combinations/hash.tsv | 5 ----- 1 file changed, 5 deletions(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index 689656d7b..6e96eb82a 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -501,8 +501,3 @@ r-base=4.3,r-ggplot2=3.4.4,r-magrittr=2.0.3,r-gridextra=2.3,r-rcolorbrewer=1.1_3 pandas=1.1.4,matchms=0.24.0,click=8.0.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 cnvkit=0.9.10,samtools=1.18 gatk4=4.4.0.0,samtools=1.18 -bwa=0.7.17,samtools=1.18 -bwa-mem2=2.2.1,samtools=1.18 -manta=1.6.0,samtools=1.18 -minimap2=2.24,samtools=1.18 -star=2.7.10a,samtools=1.18,gawk=5.1.0 From 3908148f6907b30efd5ece48026253829c5c9618 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Thu, 30 Nov 2023 13:14:19 +0100 Subject: [PATCH 6/6] move gatk to a separate PR --- combinations/hash.tsv | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index e2586a30e..213963511 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -500,9 +500,8 @@ dragmap=1.3.0,samtools=1.18,pigz=2.8 r-base=4.3,r-ggplot2=3.4.4,r-magrittr=2.0.3,r-gridextra=2.3,r-rcolorbrewer=1.1_3,r-data.table=1.14.8 pandas=1.1.4,matchms=0.24.0,click=8.0.1 quay.io/bioconda/base-glibc-busybox-bash:latest 1 cnvkit=0.9.10,samtools=1.18 -gatk4=4.4.0.0,samtools=1.18 star=2.7.10a,samtools=1.18,gawk=5.1.0 bwa=0.7.17,samtools=1.18 bwa-mem2=2.2.1,samtools=1.18 manta=1.6.0,samtools=1.18 -minimap2=2.24,samtools=1.18 \ No newline at end of file +minimap2=2.24,samtools=1.18