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Bulk fix tests #205

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6d8abdd
patch fgumi modules
matthdsm Oct 20, 2026
6d0bc7c
fix local module tests
matthdsm Oct 20, 2026
6664b22
fix local subworkflows tests
matthdsm Oct 20, 2026
562fd68
fix defaults test
matthdsm Oct 20, 2026
a3c3e75
fix workflow tests
matthdsm Oct 20, 2026
7937bc8
fix linting
matthdsm Oct 20, 2026
21df616
update bamsormadup module
matthdsm Oct 20, 2026
7542a82
Update container defs from upstream
matthdsm Oct 20, 2026
1e6f1bb
Update test resources
matthdsm Oct 20, 2026
fd7d00c
update test resources
matthdsm Oct 20, 2026
a7b8078
update nft-utils
matthdsm Oct 20, 2026
3b6b99a
fix test
matthdsm Oct 20, 2026
696eedf
fix rna test
matthdsm Oct 20, 2026
2ab6512
add gtf file to tests
matthdsm Oct 20, 2026
6a95a4e
rna snap
matthdsm Oct 20, 2026
7d9c253
fix linting issues
matthdsm Oct 21, 2026
21dc8e5
update pixi lock, update workflow snap
matthdsm Oct 21, 2026
b36ed0f
update default test snap
matthdsm Oct 21, 2026
3a6969a
Merge branch 'dev' into chore/fix-tests
matthdsm Oct 21, 2026
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8 changes: 8 additions & 0 deletions conf/containers_conda_lock_files_amd64.config
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process { withName: 'BIOBAMBAM_BAMSORMADUP' { conda = 'modules/nf-core/biobambam/bamsormadup/.conda-lock/linux_amd64-bd-f2942b2c30c9eb0a_1.txt' } }
process { withName: 'BOWTIE2_ALIGN' { conda = 'modules/nf-core/bowtie2/align/.conda-lock/linux_amd64-bd-dbd18842ad7cb278_1.txt' } }
process { withName: 'BWAMEM3_MEM' { conda = 'modules/nf-core/bwamem3/mem/.conda-lock/linux_amd64-bd-b08ae21c54a338c8_1.txt' } }
process { withName: 'FASTP' { conda = 'modules/nf-core/fastp/.conda-lock/linux_amd64-bd-df415eab5e33cb11_1.txt' } }
Expand All @@ -9,4 +10,11 @@ process { withName: 'FGUMI_SIMPLEX' { conda = 'modules/nf-core/fgumi/simplex/.co
process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } }
process { withName: 'MULTIQCSAV' { conda = 'modules/nf-core/multiqcsav/.conda-lock/linux_amd64-bd-9b10d606ce2f36b6_1.txt' } }
process { withName: 'RIKER_MULTI' { conda = 'modules/nf-core/riker/multi/.conda-lock/linux_amd64-bd-fc5310a356298f75_1.txt' } }
process { withName: 'SAMTOOLS_CONVERT' { conda = 'modules/nf-core/samtools/convert/.conda-lock/linux_amd64-bd-8a3ddf262165ba23_1.txt' } }
process { withName: 'SAMTOOLS_COVERAGE' { conda = 'modules/nf-core/samtools/coverage/.conda-lock/linux_amd64-bd-8a3ddf262165ba23_1.txt' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { conda = 'modules/nf-core/samtools/flagstat/.conda-lock/linux_amd64-bd-8a3ddf262165ba23_1.txt' } }
process { withName: 'SAMTOOLS_IDXSTATS' { conda = 'modules/nf-core/samtools/idxstats/.conda-lock/linux_amd64-bd-8a3ddf262165ba23_1.txt' } }
process { withName: 'SAMTOOLS_SORMADUP' { conda = 'modules/nf-core/samtools/sormadup/.conda-lock/linux_amd64-bd-8a3ddf262165ba23_1.txt' } }
process { withName: 'SAMTOOLS_SORT' { conda = 'modules/nf-core/samtools/sort/.conda-lock/linux_amd64-bd-8a3ddf262165ba23_1.txt' } }
process { withName: 'SAMTOOLS_STATS' { conda = 'modules/nf-core/samtools/stats/.conda-lock/linux_amd64-bd-8a3ddf262165ba23_1.txt' } }
process { withName: 'STROBEALIGN' { conda = 'modules/nf-core/strobealign/.conda-lock/linux_amd64-bd-90eb6a088ad3d321_1.txt' } }
7 changes: 7 additions & 0 deletions conf/containers_conda_lock_files_arm64.config
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Expand Up @@ -9,4 +9,11 @@ process { withName: 'FGUMI_SIMPLEX' { conda = 'modules/nf-core/fgumi/simplex/.co
process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } }
process { withName: 'MULTIQCSAV' { conda = 'modules/nf-core/multiqcsav/.conda-lock/linux_arm64-bd-077315907ed11315_1.txt' } }
process { withName: 'RIKER_MULTI' { conda = 'modules/nf-core/riker/multi/.conda-lock/linux_arm64-bd-b407026cbdb7f300_1.txt' } }
process { withName: 'SAMTOOLS_CONVERT' { conda = 'modules/nf-core/samtools/convert/.conda-lock/linux_arm64-bd-4003425f22200067_1.txt' } }
process { withName: 'SAMTOOLS_COVERAGE' { conda = 'modules/nf-core/samtools/coverage/.conda-lock/linux_arm64-bd-4003425f22200067_1.txt' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { conda = 'modules/nf-core/samtools/flagstat/.conda-lock/linux_arm64-bd-4003425f22200067_1.txt' } }
process { withName: 'SAMTOOLS_IDXSTATS' { conda = 'modules/nf-core/samtools/idxstats/.conda-lock/linux_arm64-bd-4003425f22200067_1.txt' } }
process { withName: 'SAMTOOLS_SORMADUP' { conda = 'modules/nf-core/samtools/sormadup/.conda-lock/linux_arm64-bd-4003425f22200067_1.txt' } }
process { withName: 'SAMTOOLS_SORT' { conda = 'modules/nf-core/samtools/sort/.conda-lock/linux_arm64-bd-4003425f22200067_1.txt' } }
process { withName: 'SAMTOOLS_STATS' { conda = 'modules/nf-core/samtools/stats/.conda-lock/linux_arm64-bd-4003425f22200067_1.txt' } }
process { withName: 'STROBEALIGN' { conda = 'modules/nf-core/strobealign/.conda-lock/linux_arm64-bd-be473d108d6e0fb8_1.txt' } }
8 changes: 8 additions & 0 deletions conf/containers_docker_amd64.config
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@@ -1,3 +1,4 @@
process { withName: 'BIOBAMBAM_BAMSORMADUP' { container = 'community.wave.seqera.io/library/biobambam:2.0.185--f2942b2c30c9eb0a' } }
process { withName: 'BOWTIE2_ALIGN' { container = 'community.wave.seqera.io/library/bowtie2_htslib_samtools_pigz:dbd18842ad7cb278' } }
process { withName: 'BWAMEM3_MEM' { container = 'community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:b08ae21c54a338c8' } }
process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:1.4.0--df415eab5e33cb11' } }
Expand All @@ -9,4 +10,11 @@ process { withName: 'FGUMI_SIMPLEX' { container = 'community.wave.seqera.io/libr
process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } }
process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:9b10d606ce2f36b6' } }
process { withName: 'RIKER_MULTI' { container = 'community.wave.seqera.io/library/riker:0.5.0--fc5310a356298f75' } }
process { withName: 'SAMTOOLS_CONVERT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--8a3ddf262165ba23' } }
process { withName: 'SAMTOOLS_COVERAGE' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--8a3ddf262165ba23' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--8a3ddf262165ba23' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--8a3ddf262165ba23' } }
process { withName: 'SAMTOOLS_SORMADUP' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--8a3ddf262165ba23' } }
process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--8a3ddf262165ba23' } }
process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--8a3ddf262165ba23' } }
process { withName: 'STROBEALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:90eb6a088ad3d321' } }
7 changes: 7 additions & 0 deletions conf/containers_docker_arm64.config
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Expand Up @@ -9,4 +9,11 @@ process { withName: 'FGUMI_SIMPLEX' { container = 'community.wave.seqera.io/libr
process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } }
process { withName: 'MULTIQCSAV' { container = 'community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:077315907ed11315' } }
process { withName: 'RIKER_MULTI' { container = 'community.wave.seqera.io/library/riker:0.5.0--b407026cbdb7f300' } }
process { withName: 'SAMTOOLS_CONVERT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--4003425f22200067' } }
process { withName: 'SAMTOOLS_COVERAGE' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--4003425f22200067' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--4003425f22200067' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--4003425f22200067' } }
process { withName: 'SAMTOOLS_SORMADUP' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--4003425f22200067' } }
process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--4003425f22200067' } }
process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.24--4003425f22200067' } }
process { withName: 'STROBEALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:be473d108d6e0fb8' } }
8 changes: 8 additions & 0 deletions conf/containers_singularity_https_amd64.config
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@@ -1,3 +1,4 @@
process { withName: 'BIOBAMBAM_BAMSORMADUP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4d/4d04c55ec247a77fa53dba65675e35e714ef614cc549f2193058e14312d2448c/data' } }
process { withName: 'BOWTIE2_ALIGN' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d4/d4990a9e13c1aad32d60f19e0ced204f2f1e231fe856290ce75713505a1bfe44/data' } }
process { withName: 'BWAMEM3_MEM' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/04/040dc4151df127b1cd36d1b3455ab712fe1a57fbfbee26385e8f7293f7e47ead/data' } }
process { withName: 'FASTP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/77/779b25fffc4544e4d4e3bebf1c1a1f2fee9166515bfa15908b2fee95f513a402/data' } }
Expand All @@ -9,4 +10,11 @@ process { withName: 'FGUMI_SIMPLEX' { container = 'https://community-cr-prod.seq
process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } }
process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c1311ac2bfb96d77487985fce321b25bbea85f574f9932b827ed6cafe7f75963/data' } }
process { withName: 'RIKER_MULTI' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/68/6889ae6fe776c1288a5d446e00cf57324e3e0a02b6f13fb8351bfb719dd4fc42/data' } }
process { withName: 'SAMTOOLS_CONVERT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c2f02ceb8cbe5aa37930dcbc0de6f1d07dfb292178c7e780c44ab2f556bf829f/data' } }
process { withName: 'SAMTOOLS_COVERAGE' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c2f02ceb8cbe5aa37930dcbc0de6f1d07dfb292178c7e780c44ab2f556bf829f/data' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c2f02ceb8cbe5aa37930dcbc0de6f1d07dfb292178c7e780c44ab2f556bf829f/data' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c2f02ceb8cbe5aa37930dcbc0de6f1d07dfb292178c7e780c44ab2f556bf829f/data' } }
process { withName: 'SAMTOOLS_SORMADUP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c2f02ceb8cbe5aa37930dcbc0de6f1d07dfb292178c7e780c44ab2f556bf829f/data' } }
process { withName: 'SAMTOOLS_SORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c2f02ceb8cbe5aa37930dcbc0de6f1d07dfb292178c7e780c44ab2f556bf829f/data' } }
process { withName: 'SAMTOOLS_STATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c2f02ceb8cbe5aa37930dcbc0de6f1d07dfb292178c7e780c44ab2f556bf829f/data' } }
process { withName: 'STROBEALIGN' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/58/58b8968bb248307d133950891a33c9e569f5f1aa729ad997d8bb1311ec7f2589/data' } }
7 changes: 7 additions & 0 deletions conf/containers_singularity_https_arm64.config
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Expand Up @@ -9,4 +9,11 @@ process { withName: 'FGUMI_SIMPLEX' { container = 'https://community-cr-prod.seq
process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } }
process { withName: 'MULTIQCSAV' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/05/053f6d8c55b57e04b654070a3bd6eaa90685590158019d35c16092d301b80cb1/data' } }
process { withName: 'RIKER_MULTI' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1e/1e6c8b6b94159eba36cb744489468edddf09202a42b09cf41af6681325b8d60a/data' } }
process { withName: 'SAMTOOLS_CONVERT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24bce03b37817d335921ac9bf9d9ca0d485d3b18926413f643b10e45ec1f5c6b/data' } }
process { withName: 'SAMTOOLS_COVERAGE' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24bce03b37817d335921ac9bf9d9ca0d485d3b18926413f643b10e45ec1f5c6b/data' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24bce03b37817d335921ac9bf9d9ca0d485d3b18926413f643b10e45ec1f5c6b/data' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24bce03b37817d335921ac9bf9d9ca0d485d3b18926413f643b10e45ec1f5c6b/data' } }
process { withName: 'SAMTOOLS_SORMADUP' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24bce03b37817d335921ac9bf9d9ca0d485d3b18926413f643b10e45ec1f5c6b/data' } }
process { withName: 'SAMTOOLS_SORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24bce03b37817d335921ac9bf9d9ca0d485d3b18926413f643b10e45ec1f5c6b/data' } }
process { withName: 'SAMTOOLS_STATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24bce03b37817d335921ac9bf9d9ca0d485d3b18926413f643b10e45ec1f5c6b/data' } }
process { withName: 'STROBEALIGN' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/54/54a576c51485cf7af3223084b2bfffabbe1c25c92c987ba564bb061ad0a16c89/data' } }
8 changes: 8 additions & 0 deletions conf/containers_singularity_oras_amd64.config
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@@ -1,3 +1,4 @@
process { withName: 'BIOBAMBAM_BAMSORMADUP' { container = 'oras://community.wave.seqera.io/library/biobambam:2.0.185--97142ab63c6fabee' } }
process { withName: 'BOWTIE2_ALIGN' { container = 'oras://community.wave.seqera.io/library/bowtie2_htslib_samtools_pigz:1d137fae829780dd' } }
process { withName: 'BWAMEM3_MEM' { container = 'oras://community.wave.seqera.io/library/bwa-mem3_htslib_samtools_findutils:fb293a77182e2fe6' } }
process { withName: 'FASTP' { container = 'oras://community.wave.seqera.io/library/fastp:1.4.0--6b9a33725b111ca0' } }
Expand All @@ -9,4 +10,11 @@ process { withName: 'FGUMI_SIMPLEX' { container = 'oras://community.wave.seqera.
process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } }
process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:a26da1aa4e8d32a6' } }
process { withName: 'RIKER_MULTI' { container = 'oras://community.wave.seqera.io/library/riker:0.5.0--494641445248cb80' } }
process { withName: 'SAMTOOLS_CONVERT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--780d5da12d0c564c' } }
process { withName: 'SAMTOOLS_COVERAGE' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--780d5da12d0c564c' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--780d5da12d0c564c' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--780d5da12d0c564c' } }
process { withName: 'SAMTOOLS_SORMADUP' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--780d5da12d0c564c' } }
process { withName: 'SAMTOOLS_SORT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--780d5da12d0c564c' } }
process { withName: 'SAMTOOLS_STATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--780d5da12d0c564c' } }
process { withName: 'STROBEALIGN' { container = 'oras://community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:38afc784dff2496a' } }
7 changes: 7 additions & 0 deletions conf/containers_singularity_oras_arm64.config
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Expand Up @@ -9,4 +9,11 @@ process { withName: 'FGUMI_SIMPLEX' { container = 'oras://community.wave.seqera.
process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } }
process { withName: 'MULTIQCSAV' { container = 'oras://community.wave.seqera.io/library/multiqc_multiqc_sav_pip_interop:d1ed21d66511158d' } }
process { withName: 'RIKER_MULTI' { container = 'oras://community.wave.seqera.io/library/riker:0.5.0--b47ea90c58131414' } }
process { withName: 'SAMTOOLS_CONVERT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--b75d2385b98b4033' } }
process { withName: 'SAMTOOLS_COVERAGE' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--b75d2385b98b4033' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--b75d2385b98b4033' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--b75d2385b98b4033' } }
process { withName: 'SAMTOOLS_SORMADUP' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--b75d2385b98b4033' } }
process { withName: 'SAMTOOLS_SORT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--b75d2385b98b4033' } }
process { withName: 'SAMTOOLS_STATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.24--b75d2385b98b4033' } }
process { withName: 'STROBEALIGN' { container = 'oras://community.wave.seqera.io/library/htslib_samtools_strobealign_pigz:90ad219a62d4fc12' } }
4 changes: 2 additions & 2 deletions conf/test.config
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@ params {

process {
resourceLimits = [
cpus: 2,
memory: 6.GB,
cpus: 4,
memory: 14.GB,
time: 6.h,
]
}
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18 changes: 9 additions & 9 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
},
"biobambam/bamsormadup": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"git_sha": "d677860352f8618d66362c3d036441f7f0729584",
"installed_by": ["modules"],
"patch": "modules/nf-core/biobambam/bamsormadup/biobambam-bamsormadup.diff"
},
Expand Down Expand Up @@ -113,41 +113,41 @@
},
"samtools/convert": {
"branch": "master",
"git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
"git_sha": "5f344f0e41fdfaf2506f89400e42a2689d6ab323",
"installed_by": ["modules"],
"patch": "modules/nf-core/samtools/convert/samtools-convert.diff"
},
"samtools/coverage": {
"branch": "master",
"git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
"git_sha": "5f344f0e41fdfaf2506f89400e42a2689d6ab323",
"installed_by": ["modules"],
"patch": "modules/nf-core/samtools/coverage/samtools-coverage.diff"
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
"git_sha": "5f344f0e41fdfaf2506f89400e42a2689d6ab323",
"installed_by": ["modules"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
"git_sha": "5f344f0e41fdfaf2506f89400e42a2689d6ab323",
"installed_by": ["modules"]
},
"samtools/sormadup": {
"branch": "master",
"git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
"git_sha": "5f344f0e41fdfaf2506f89400e42a2689d6ab323",
"installed_by": ["modules"],
"patch": "modules/nf-core/samtools/sormadup/samtools-sormadup.diff"
},
"samtools/sort": {
"branch": "master",
"git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
"git_sha": "5f344f0e41fdfaf2506f89400e42a2689d6ab323",
"installed_by": ["modules"],
"patch": "modules/nf-core/samtools/sort/samtools-sort.diff"
},
"samtools/stats": {
"branch": "master",
"git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
"git_sha": "5f344f0e41fdfaf2506f89400e42a2689d6ab323",
"installed_by": ["modules"],
"patch": "modules/nf-core/samtools/stats/samtools-stats.diff"
},
Expand All @@ -159,7 +159,7 @@
},
"star/align": {
"branch": "master",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"git_sha": "55b55bf2e58958b0c7b96ac60cd4b38d7724c7a5",
"installed_by": ["modules"],
"patch": "modules/nf-core/star/align/star-align.diff"
},
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