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build: Fix modules.json and bump subworkflows
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@edmundmiller
edmundmiller committed Mar 20, 2024
1 parent cbf6bce commit 6f11e07
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Showing 35 changed files with 2,162 additions and 261 deletions.
45 changes: 18 additions & 27 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@
},
"bowtie2/align": {
"branch": "master",
"git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
"installed_by": ["fastq_align_bowtie2", "modules"]
"git_sha": "0fe30831abbc2ed115e46e92330edf38f56edc3d",
"installed_by": ["fastq_align_bowtie2"]
},
"bowtie2/build": {
"branch": "master",
Expand All @@ -47,8 +47,8 @@
},
"bwa/mem": {
"branch": "master",
"git_sha": "1e2b7fb7106852388610c0360d234b0829eb980e",
"installed_by": ["fastq_align_bwa", "modules"]
"git_sha": "b97197968ac12dde2463fa54541f6350c46f2035",
"installed_by": ["fastq_align_bwa"]
},
"bwamem2/index": {
"branch": "master",
Expand All @@ -70,11 +70,6 @@
"git_sha": "02fd5bd7275abad27aad32d5c852e0a9b1b98882",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "1b0ffa4e5aed5b7e3cd4311af31bd3b2c8345051",
Expand Down Expand Up @@ -119,27 +114,27 @@
"hisat2/align": {
"branch": "master",
"git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1",
"installed_by": ["fastq_align_hisat2", "modules"]
"installed_by": ["fastq_align_hisat2"]
},
"homer/findpeaks": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["homer/groseq"]
"installed_by": ["groseq", "homer/groseq"]
},
"homer/maketagdirectory": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["homer/groseq"]
"installed_by": ["groseq", "homer/groseq"]
},
"homer/makeucscfile": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["homer/groseq"]
"installed_by": ["groseq", "homer/groseq"]
},
"homer/pos2bed": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["homer/groseq"]
"installed_by": ["groseq", "homer/groseq"]
},
"multiqc": {
"branch": "master",
Expand Down Expand Up @@ -194,7 +189,7 @@
},
"samtools/sort": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/stats": {
Expand All @@ -209,7 +204,7 @@
},
"umitools/dedup": {
"branch": "master",
"git_sha": "ff7e93715a2acecf3f143ec78c9858deba2984d0",
"git_sha": "3bd4f34e3093c2a16e6a8eefc22242b9b94641db",
"installed_by": ["bam_dedup_stats_samtools_umitools"]
},
"untar": {
Expand All @@ -228,38 +223,34 @@
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["fastq_align_bowtie2", "fastq_align_bwa", "fastq_align_hisat2", "subworkflows"]
"git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
"installed_by": ["fastq_align_bowtie2", "fastq_align_bwa", "fastq_align_hisat2"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools", "subworkflows"]
"installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools"]
},
"fastq_align_bowtie2": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"git_sha": "0fe30831abbc2ed115e46e92330edf38f56edc3d",
"installed_by": ["subworkflows"]
},
"fastq_align_bwa": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"git_sha": "b97197968ac12dde2463fa54541f6350c46f2035",
"installed_by": ["subworkflows"]
},
"fastq_align_hisat2": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"git_sha": "701ae347c4508fba1b7d65262596f278b6a11cb6",
"installed_by": ["subworkflows"]
},
"homer/groseq": {
"branch": "master",
"git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
"installed_by": ["subworkflows"]
}
}
},
"subworkflows": {
"nf-core": {
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
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26 changes: 22 additions & 4 deletions modules/nf-core/bowtie2/align/main.nf
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5 changes: 5 additions & 0 deletions modules/nf-core/bowtie2/align/tests/cram_crai.config
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