BAM/CRAM support

For milestone 2.2.0

Author: charles-plessy

CHANGELOG.md

@@ -3,6 +3,24 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v2.2.0dev](https://github.com/nf-core/pairgenomealign/releases/tag/2.2.0)
+
+### `Added`
+
+- Support for export to BAM and CRAM formats ([#31](https://github.com/nf-core/pairgenomealign/issues/31)) ([#43](https://github.com/nf-core/pairgenomealign/issues/43)).
+
+### `Dependencies`
+
+| Dependency       | Old version | New version |
+| ---------------- | ----------- | ----------- |
+| `SAMTOOLS_BGZIP` |             | 1.21        |
+| `SAMTOOLS_DICT`  |             | 1.21        |
+| `SAMTOOLS_FAIDX` |             | 1.21        |
+
+### `Fixed`
+
+- Remove noisy tag in the `MULTIQC_ASSEMBLYSCAN_PLOT_DATA` local module ([#64](https://github.com/nf-core/pairgenomealign/issues/64)).
+
 ## [v2.1.0](https://github.com/nf-core/pairgenomealign/releases/tag/2.1.0) "Goya champuru" - [May 16th 2025]
 
 ### `Added`

CITATIONS.md

@@ -26,6 +26,10 @@
 
   > Frith MC, Shaw J, Spouge JL. How to optimally sample a sequence for rapid analysis. doi: 10.1093/bioinformatics/btad057 PubMed PMID: 36702468 (Describes the lastdb -u RY sparsity options.)
 
+- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)
+
+  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

README.md

@@ -29,6 +29,7 @@ The main steps of the pipeline are:
 2. Genome indexing ([`lastdb`](https://gitlab.com/mcfrith/last/-/blob/main/doc/lastdb.rst)).
 3. Genome pairwise alignments ([`lastal`](https://gitlab.com/mcfrith/last/-/blob/main/doc/lastal.rst)).
 4. Alignment plotting ([`last-dotplot`](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst)).
+5. Alignment export to various formats with [`maf-convert`](https://gitlab.com/mcfrith/last/-/blob/main/doc/maf-convert.rst), plus [`Samtools`](https://www.htslib.org/) for SAM/BAM/CRAM.
 
 The pipeline can generate four kinds of outputs, called _many-to-many_, _many-to-one_, _one-to-many_ and _one-to-one_, depending on whether sequences of one genome are allowed match the other genome multiple times or not.
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/releases/tag/2.1.0"
+  This report has been generated by the <a href="https://github.com/nf-core/pairgenomealign/tree/dev"
   target="_blank">nf-core/pairgenomealign</a> analysis pipeline. For information about
-  how to interpret these results, please see the <a href="https://nf-co.re/pairgenomealign/2.1.0/docs/output"
+  how to interpret these results, please see the <a href="https://nf-co.re/pairgenomealign/dev/docs/output"
   target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pairgenomealign-methods-description":

conf/modules.config

@@ -126,4 +126,24 @@ process {
         ]
     }
 
+    withName: 'SAMTOOLS_BGZIP' {
+        publishDir = publishDir + [
+            path: { "${params.outdir}/alignment" }
+        ]
+    }
+
+    withName: 'SAMTOOLS_FAIDX' {
+        publishDir = [
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename.equals('versions.yml') || filename.endsWith('.sizes')) ? null : filename }
+        ]
+    }
+
+    withName: 'SAMTOOLS_DICT' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+
 }

docs/output.md

@@ -41,7 +41,7 @@ Basic statistics on nucleotide content and contig length are collected for align
   - `*.m2o_aln.maf.gz` is the _**many-to-one**_ alignment regions of the _target_ genome are matched at most once by the _query_ genome. (optional through the `--m2m` option)
   - `*.o2m_aln.maf.gz` is the _**one-to-many**_ alignment between the _target_ and _query_ genomes. (optional through the `--m2m` option)
   - `*.o2o_aln.maf.gz` is the _**one-to-one**_ alignment between the _target_ and _query_ genomes.
-  - For each MAF file there will be an additional file in a format such as Axt, Chain, GFF or SAM if you used the `--export_aln_to` parameter. These files are always compressed.
+  - For each _**one-to-one**_ alignment there will be an additional file in a format such as Axt, Chain, GFF or SAM/BAM/CRAM if you used the `--export_aln_to` parameter. These extra files are always compressed with gzip when their format is text-based.
 
 </details>
 

modules.json

@@ -50,6 +50,21 @@
                         "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
                         "installed_by": ["modules"]
                     },
+                    "samtools/bgzip": {
+                        "branch": "master",
+                        "git_sha": "f2dba87f4793a4015f0611cd1743cbfb598c74e7",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/dict": {
+                        "branch": "master",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "installed_by": ["modules"]
+                    },
                     "seqtk/cutn": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",

modules/local/multiqc_assemblyscan_plot_data/main.nf

@@ -1,5 +1,4 @@
 process MULTIQC_ASSEMBLYSCAN_PLOT_DATA {
-    tag "${json.baseName}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"