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‎.nf-core.yml‎

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name: bactmap
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description: A mapping-based pipeline for bacterial whole genome sequences
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author: Andries J. van Tonder
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version: 2.0.0dev
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version: 2.0.0
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force: true
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outdir: .
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skip_features: []

‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## v2.0.0dev - [date]
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## 2.0.0 - Titanium Bird - 2025-09-15
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nf-core/bactmap release v2.0.0. The pipeline has been completely rewritten using a fresh template created with [nf-core](https://nf-co.re/).
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‎assets/multiqc_config.yml‎

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# multiqc_config.yml
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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/bactmap/tree/dev" target="_blank">nf-core/bactmap</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/bactmap/dev/docs/output" target="_blank">documentation</a>.
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This report has been generated by the <a href="https://github.com/nf-core/bactmap/releases/tag/2.0.0"
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target="_blank">nf-core/bactmap</a> analysis pipeline. For information about how
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to interpret these results, please see the <a href="https://nf-co.re/bactmap/2.0.0/docs/output"
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target="_blank">documentation</a>.
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# Report section order
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report_section_order:
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anchor: "filtlong"
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target: "Filtlong"
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doi: "10.1371/journal.pcbi.1010905"
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info: "This section of the report shows Filtlong results for reads after length filtering."
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info: "This section of the report shows Filtlong results for reads after length
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filtering."
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path_filters:
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- "*filtlong/*"
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extra: |
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anchor: "samtools"
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target: "SAMTools"
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doi: "10.1093/bioinformatics/btp352"
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info: "This section of the report shows SAMTools counts/statistics after mapping with Bowtie 2/BWA 2 mem."
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info: "This section of the report shows SAMTools counts/statistics after mapping
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with Bowtie 2/BWA 2 mem."
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path_filters:
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- "*.stats"
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- "bcftools":
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name: "BCFTools"
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anchor: "bcftools"
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target: "BCFTools"
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doi: "10.1093/bioinformatics/btp352"
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info: "This section of the report shows BCFTools stats results for the called variants."
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info: "This section of the report shows BCFTools stats results for the called
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variants."
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path_filters:
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- "*.txt"
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‎modules.json‎

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},
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"bcftools/filter": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
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"installed_by": ["modules"]
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},
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"bcftools/index": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
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"installed_by": ["bam_variant_calling_sort_freebayes_bcftools"]
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},
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"bcftools/query": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
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"installed_by": ["modules"]
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},
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"bcftools/sort": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
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"installed_by": ["bam_variant_calling_sort_freebayes_bcftools"]
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},
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"bcftools/stats": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
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"installed_by": ["modules"]
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},
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"bedtools/subtract": {
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},
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"fastp": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["modules"]
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},
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"fastqc": {
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},
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"samtools/faidx": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["modules"]
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},
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"samtools/flagstat": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/idxstats": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["modules"]
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},
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"samtools/sort": {
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"branch": "master",
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"git_sha": "e89ff68a46b848c4d8aabb8569767516d46db319",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["modules"]
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["bam_stats_samtools", "modules"]
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},
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"seqtk/comp": {
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"nf-core": {
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"bam_stats_samtools": {
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"branch": "master",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["subworkflows"]
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},
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"utils_nextflow_pipeline": {

‎modules/nf-core/bcftools/filter/environment.yml‎

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‎modules/nf-core/bcftools/filter/main.nf‎

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