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Update Parabricks to 4.8.0-1 (with samtools 1.25 and Picard 3.5.0) #641

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Merged
eduard-watchmaker merged 5 commits into from
Nov 11, 2026
+10,895 −1,305
Merged

Update Parabricks to 4.8.0-1 (with samtools 1.25 and Picard 3.5.0) #641

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ddf3ca8
chore: update Parabricks (4.8.0-1), samtools (1.25) and Picard (3.5.0…
eduard-watchmaker Nov 11, 2026
bde810a
chore: update Parabricks to 4.8.0-1 with samtools 1.25 and Picard 3.5.0
eduard-watchmaker Nov 11, 2026
50139bd
Merge taps_v2 (nf-core/tools 4.2.2 template update) into parabricks-4.8
eduard-watchmaker Nov 11, 2026
336a66a
test: fix the bwamem TAPS GPU snapshot
eduard-watchmaker Nov 11, 2026
4cb0ac8
test: order the bwamem TAPS GPU snapshot versions as nf-test does
eduard-watchmaker Nov 11, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Threaded a combined `[ meta, fasta, fai ]` channel through the alignment subworkflows
- 🔧 Add [methurator](https://vibtobilab.github.io/methurator/latest/) as an additional QC tool for both the Bismark and bwa-meth subworkflows.
- 🔧 Update the `bwameth/align` and `bwameth/index` modules to bwa-meth 0.2.10 (consistent read-name handling and FASTQ comment-tag propagation upstream) and samtools 1.25 ([#637](https://github.com/nf-core/methylseq/pull/637))
- 🔧 Update Parabricks to 4.8.0-1 (`parabricks/fq2bam` and `parabricks/fq2bammeth`), samtools to 1.25 and Picard to 3.5.0 in the GPU and bwa-mem alignment paths, with the nf-core modules and subworkflows they use (`fastq_align_dedup_bwameth`, `fastq_align_dedup_bwamem`, `fastq_align_bwa`, `bam_sort_stats_samtools`, `bam_stats_samtools`, `bam_methyldackel`). `samtools/faidx` moves to samtools 1.25 too. Results are unchanged, except that Parabricks 4.8 `fq2bam` adds the `MC` tag to unmapped reads with a mapped mate. A new GPU test covers `--aligner bwamem --taps` (`parabricks/fq2bam`)
- 🔄 Update template to nf-core/tools v4.2.1 (includes v4.1.0); minimum Nextflow version is now 25.10.4 and nf-schema is bumped to 2.7.3 ([#634](https://github.com/nf-core/methylseq/pull/634))
- 🔧 Merge the nf-core/tools v4.0.2 template; drops the Slack/Teams webhook notification feature (`imNotification`/`hook_url`) in line with the template ([#606](https://github.com/nf-core/methylseq/pull/606))

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8 changes: 8 additions & 0 deletions conf/containers_conda_lock_files_amd64.config
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Expand Up @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { conda = 'modules/nf-core/bwameth/align/.co
process { withName: 'BWAMETH_INDEX' { conda = 'modules/nf-core/bwameth/index/.conda-lock/linux_amd64-bd-a589797f382631bc_1.txt' } }
process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { conda = 'modules/nf-core/picard/addorreplacereadgroups/.conda-lock/linux_amd64-bd-be20f299a1924f0d_1.txt' } }
process { withName: 'PICARD_MARKDUPLICATES' { conda = 'modules/nf-core/picard/markduplicates/.conda-lock/linux_amd64-bd-be20f299a1924f0d_1.txt' } }
process { withName: 'RASTAIR2_CALL' { conda = 'modules/nf-core/rastair2/call/.conda-lock/linux_amd64-bd-4ffd26b40813e268_1.txt' } }
process { withName: 'RASTAIR2_MBIAS' { conda = 'modules/nf-core/rastair2/mbias/.conda-lock/linux_amd64-bd-4ffd26b40813e268_1.txt' } }
process { withName: 'SAMTOOLS_FAIDX' { conda = 'modules/nf-core/samtools/faidx/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { conda = 'modules/nf-core/samtools/flagstat/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } }
process { withName: 'SAMTOOLS_IDXSTATS' { conda = 'modules/nf-core/samtools/idxstats/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } }
process { withName: 'SAMTOOLS_INDEX' { conda = 'modules/nf-core/samtools/index/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } }
process { withName: 'SAMTOOLS_SORT' { conda = 'modules/nf-core/samtools/sort/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } }
process { withName: 'SAMTOOLS_STATS' { conda = 'modules/nf-core/samtools/stats/.conda-lock/linux_amd64-bd-704fb80d75745bd4_7.txt' } }
8 changes: 8 additions & 0 deletions conf/containers_conda_lock_files_arm64.config
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Expand Up @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { conda = 'modules/nf-core/bwameth/align/.co
process { withName: 'BWAMETH_INDEX' { conda = 'modules/nf-core/bwameth/index/.conda-lock/linux_arm64-bd-d9a640227e3efef9_1.txt' } }
process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { conda = 'modules/nf-core/picard/addorreplacereadgroups/.conda-lock/linux_arm64-bd-5516268008db5ab4_1.txt' } }
process { withName: 'PICARD_MARKDUPLICATES' { conda = 'modules/nf-core/picard/markduplicates/.conda-lock/linux_arm64-bd-5516268008db5ab4_1.txt' } }
process { withName: 'RASTAIR2_CALL' { conda = 'modules/nf-core/rastair2/call/.conda-lock/linux_arm64-bd-0f7189390ccfdc4d_1.txt' } }
process { withName: 'RASTAIR2_MBIAS' { conda = 'modules/nf-core/rastair2/mbias/.conda-lock/linux_arm64-bd-0f7189390ccfdc4d_1.txt' } }
process { withName: 'SAMTOOLS_FAIDX' { conda = 'modules/nf-core/samtools/faidx/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { conda = 'modules/nf-core/samtools/flagstat/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } }
process { withName: 'SAMTOOLS_IDXSTATS' { conda = 'modules/nf-core/samtools/idxstats/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } }
process { withName: 'SAMTOOLS_INDEX' { conda = 'modules/nf-core/samtools/index/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } }
process { withName: 'SAMTOOLS_SORT' { conda = 'modules/nf-core/samtools/sort/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } }
process { withName: 'SAMTOOLS_STATS' { conda = 'modules/nf-core/samtools/stats/.conda-lock/linux_arm64-bd-944a4060c62320c2_8.txt' } }
8 changes: 8 additions & 0 deletions conf/containers_docker_amd64.config
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Expand Up @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'community.wave.seqera.io/libr
process { withName: 'BWAMETH_INDEX' { container = 'community.wave.seqera.io/library/bwameth:0.2.10--a589797f382631bc' } }
process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2' } }
process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'community.wave.seqera.io/library/picard:3.5.0--be20f299a1924f0d' } }
process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.5.0--be20f299a1924f0d' } }
process { withName: 'RASTAIR2_CALL' { container = 'community.wave.seqera.io/library/htslib_rastair:4ffd26b40813e268' } }
process { withName: 'RASTAIR2_MBIAS' { container = 'community.wave.seqera.io/library/htslib_rastair:4ffd26b40813e268' } }
process { withName: 'SAMTOOLS_FAIDX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } }
process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } }
process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } }
process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--704fb80d75745bd4' } }
8 changes: 8 additions & 0 deletions conf/containers_docker_arm64.config
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Expand Up @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'community.wave.seqera.io/libr
process { withName: 'BWAMETH_INDEX' { container = 'community.wave.seqera.io/library/bwameth:0.2.10--d9a640227e3efef9' } }
process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68' } }
process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'community.wave.seqera.io/library/picard:3.5.0--5516268008db5ab4' } }
process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.5.0--5516268008db5ab4' } }
process { withName: 'RASTAIR2_CALL' { container = 'community.wave.seqera.io/library/htslib_rastair:0f7189390ccfdc4d' } }
process { withName: 'RASTAIR2_MBIAS' { container = 'community.wave.seqera.io/library/htslib_rastair:0f7189390ccfdc4d' } }
process { withName: 'SAMTOOLS_FAIDX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } }
process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } }
process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } }
process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.25--944a4060c62320c2' } }
8 changes: 8 additions & 0 deletions conf/containers_singularity_https_amd64.config
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Expand Up @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'https://community-cr-prod.seq
process { withName: 'BWAMETH_INDEX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/44/4405ebf9fd0b415a9e28b0cb503b11af0e86c88ab335b098ff4cf48f8f0162e1/data' } }
process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data' } }
process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b474c6f12c0502377b95062b75ef4b7778864b1353c7fc1d5a3b1f3b3017fd2e/data' } }
process { withName: 'PICARD_MARKDUPLICATES' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b474c6f12c0502377b95062b75ef4b7778864b1353c7fc1d5a3b1f3b3017fd2e/data' } }
process { withName: 'RASTAIR2_CALL' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/50/50c87ecbec7ea76f99ff4ad84e16f083c0b74651bf813d9158b1004234f6feca/data' } }
process { withName: 'RASTAIR2_MBIAS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/50/50c87ecbec7ea76f99ff4ad84e16f083c0b74651bf813d9158b1004234f6feca/data' } }
process { withName: 'SAMTOOLS_FAIDX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } }
process { withName: 'SAMTOOLS_INDEX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } }
process { withName: 'SAMTOOLS_SORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } }
process { withName: 'SAMTOOLS_STATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/87/87660348a4d032cc08d6ac8101ff9d4d27164300d39c9472043bb5001f9ba801/data' } }
8 changes: 8 additions & 0 deletions conf/containers_singularity_https_arm64.config
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Expand Up @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'https://community-cr-prod.seq
process { withName: 'BWAMETH_INDEX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/12bda1a46bacec84b4724f48b09117afc6e68a40c59d442bb874c638e19ee571/data' } }
process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data' } }
process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/35/35ed881e77f6b66f1b9204394c8909fd66da367891434a81f536704a13fad3c3/data' } }
process { withName: 'PICARD_MARKDUPLICATES' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/35/35ed881e77f6b66f1b9204394c8909fd66da367891434a81f536704a13fad3c3/data' } }
process { withName: 'RASTAIR2_CALL' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/11/11261c0ef97d532effc21421bd7c824749330dba152db93e4d5d583c362e0620/data' } }
process { withName: 'RASTAIR2_MBIAS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/11/11261c0ef97d532effc21421bd7c824749330dba152db93e4d5d583c362e0620/data' } }
process { withName: 'SAMTOOLS_FAIDX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } }
process { withName: 'SAMTOOLS_INDEX' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } }
process { withName: 'SAMTOOLS_SORT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } }
process { withName: 'SAMTOOLS_STATS' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/514f17bd9e1c013214957c34ea8bc446a86e4350bb6da41c126f55a27618932d/data' } }
8 changes: 8 additions & 0 deletions conf/containers_singularity_oras_amd64.config
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Expand Up @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'oras://community.wave.seqera.
process { withName: 'BWAMETH_INDEX' { container = 'oras://community.wave.seqera.io/library/bwameth:0.2.10--77efa7670825aae0' } }
process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd' } }
process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'oras://community.wave.seqera.io/library/picard:3.5.0--89375ac386b71342' } }
process { withName: 'PICARD_MARKDUPLICATES' { container = 'oras://community.wave.seqera.io/library/picard:3.5.0--89375ac386b71342' } }
process { withName: 'RASTAIR2_CALL' { container = 'oras://community.wave.seqera.io/library/htslib_rastair:8f58b5250bf317c8' } }
process { withName: 'RASTAIR2_MBIAS' { container = 'oras://community.wave.seqera.io/library/htslib_rastair:8f58b5250bf317c8' } }
process { withName: 'SAMTOOLS_FAIDX' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } }
process { withName: 'SAMTOOLS_INDEX' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } }
process { withName: 'SAMTOOLS_SORT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } }
process { withName: 'SAMTOOLS_STATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--2d67558d8613e11c' } }
8 changes: 8 additions & 0 deletions conf/containers_singularity_oras_arm64.config
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Expand Up @@ -12,5 +12,13 @@ process { withName: 'BWAMETH_ALIGN' { container = 'oras://community.wave.seqera.
process { withName: 'BWAMETH_INDEX' { container = 'oras://community.wave.seqera.io/library/bwameth:0.2.10--449d0d6bffe0d0ea' } }
process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035' } }
process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
process { withName: 'PICARD_ADDORREPLACEREADGROUPS' { container = 'oras://community.wave.seqera.io/library/picard:3.5.0--51fe15653ca25a7c' } }
process { withName: 'PICARD_MARKDUPLICATES' { container = 'oras://community.wave.seqera.io/library/picard:3.5.0--51fe15653ca25a7c' } }
process { withName: 'RASTAIR2_CALL' { container = 'oras://community.wave.seqera.io/library/htslib_rastair:42892508b9c8b619' } }
process { withName: 'RASTAIR2_MBIAS' { container = 'oras://community.wave.seqera.io/library/htslib_rastair:42892508b9c8b619' } }
process { withName: 'SAMTOOLS_FAIDX' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } }
process { withName: 'SAMTOOLS_INDEX' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } }
process { withName: 'SAMTOOLS_SORT' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } }
process { withName: 'SAMTOOLS_STATS' { container = 'oras://community.wave.seqera.io/library/htslib_samtools:1.25--3b9e70f96c37875a' } }
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