pull from upstream and merge conflicts

CHANGELOG.md

@@ -7,14 +7,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#674](https://github.com/nf-core/mag/pull/674) - Added `--longread_adaptertrimming_tool` Where user can chose between porechop_abi (default) and porechop (added by @muabnezor)
+
 ### `Changed`
 
+- [#674](https://github.com/nf-core/mag/pull/674) - Changed to porechop-abi as default adapter trimming tool for long reads. User can still use porechop if preferred (added by @muabnezor)
+
 ### `Fixed`
 
+- [#674](https://github.com/nf-core/mag/pull/674) - Make longread preprocessing a subworkflow (added by @muabnezor)
+- [#674](https://github.com/nf-core/mag/pull/674) - Add porechop and filtlong logs to multiqc (added by @muabnezor)
+- [#674](https://github.com/nf-core/mag/pull/674) - Change local filtlong module to the official nf-core/filtlong module (added by @muabnezor)
 - [#690](https://github.com/nf-core/mag/pull/690) - MaxBin2 is using the abundance information from different samples now as expected (reported by @uel3 and fixed by @d4straub)
 
 ### `Dependencies`
 
+| Tool         | Previous version | New version |
+| ------------ | ---------------- | ----------- |
+| Porechop_ABI |                  | 0.5.0       |
+| Filtlong     | 0.2.0            | 0.2.1       |
+
 ### `Deprecated`
 
 ## 3.1.0 [2024-10-04]

CITATIONS.md

@@ -116,6 +116,8 @@
 
 - [Porechop](https://github.com/rrwick/Porechop)
 
+- [Porechop-abi](https://github.com/bonsai-team/Porechop_ABI)
+
 - [Prodigal](https://pubmed.ncbi.nlm.nih.gov/20211023/)
 
   > Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11:119. doi: 10.1186/1471-2105-11-119. PMID: 20211023; PMCID: PMC2848648.

README.md

@@ -90,6 +90,7 @@ Other code contributors include:
 - [Jim Downie](https://github.com/prototaxites)
 - [Phil Palmer](https://github.com/PhilPalmer)
 - [@willros](https://github.com/willros)
+- [Adam Rosenbaum](https://github.com/muabnezor)
 
 Long read processing was inspired by [caspargross/HybridAssembly](https://github.com/caspargross/HybridAssembly) written by Caspar Gross [@caspargross](https://github.com/caspargross)
 

assets/multiqc_config.yml

@@ -25,6 +25,8 @@ run_modules:
   - quast
   - kraken
   - prokka
+  - porechop
+  - filtlong
 
 ## Module order
 top_modules:
@@ -35,6 +37,7 @@ top_modules:
   - "fastp"
   - "adapterRemoval"
   - "porechop"
+  - "filtlong"
   - "fastqc":
       name: "FastQC: after preprocessing"
       info: "After trimming and, if requested, contamination removal."
@@ -109,6 +112,9 @@ sp:
     fn_re: ".*[kraken2|centrifuge].*report.txt"
   quast:
     fn_re: "report.*.tsv"
+  filtlong:
+    num_lines: 20
+    fn_re: ".*_filtlong.log"
 
 ## File name cleaning
 extra_fn_clean_exts:

conf/modules.config

@@ -171,20 +171,36 @@ process {
         publishDir = [
             path: { "${params.outdir}/QC_longreads/porechop" },
             mode: params.publish_dir_mode,
-            pattern: "*_trimmed.fastq",
+            pattern: "*_porechop_trimmed.fastq.gz",
             enabled: params.save_porechop_reads
         ]
-        ext.prefix = { "${meta.id}_run${meta.run}_trimmed" }
+        ext.prefix = { "${meta.id}_run${meta.run}_porechop_trimmed" }
+    }
+
+    withName: PORECHOP_ABI {
+        publishDir = [
+                path: { "${params.outdir}/QC_longreads/porechop" },
+                mode: params.publish_dir_mode,
+                pattern: "*_porechop-abi_trimmed.fastq.gz",
+                enabled: params.save_porechop_reads
+            ]
+        ext.prefix = { "${meta.id}_run${meta.run}_porechop-abi_trimmed" }
     }
 
     withName: FILTLONG {
+        ext.args = [
+            "--min_length ${params.longreads_min_length}",
+            "--keep_percent ${params.longreads_keep_percent}",
+            "--trim",
+            "--length_weight ${params.longreads_length_weight}"
+        ].join(' ').trim()
         publishDir = [
-            path: { "${params.outdir}/QC_longreads/Filtlong" },
-            mode: params.publish_dir_mode,
-            pattern: "*_lr_filtlong.fastq.gz",
-            enabled: params.save_filtlong_reads
-        ]
-        ext.prefix = { "${meta.id}_run${meta.run}_lengthfiltered" }
+                path: { "${params.outdir}/QC_longreads/Filtlong" },
+                mode: params.publish_dir_mode,
+                pattern: "*_filtlong.fastq.gz",
+                enabled: params.save_filtlong_reads
+            ]
+        ext.prefix = { "${meta.id}_run${meta.run}_filtlong" }
     }
 
     withName: NANOLYSE {

docs/output.md

@@ -113,6 +113,19 @@ The pipeline uses Nanolyse to map the reads against the Lambda phage and removes
 
 The pipeline uses filtlong and porechop to perform quality control of the long reads that are eventually provided with the TSV input file.
 
+<details markdown="1">
+<summary>Output files</summary>
+
+- `QC_longreads/porechop/`
+  - `[sample]_[run]_porechop_trimmed.fastq.gz`: If `--longread_adaptertrimming_tool 'porechop'`, the adapter trimmed FASTQ files from porechop
+  - `[sample]_[run]_porechop-abi_trimmed.fastq.gz`: If `--longread_adaptertrimming_tool 'porechop_abi'`, the adapter trimmed FASTQ files from porechop_ABI
+- `QC_longreads/filtlong/`
+  - `[sample]_[run]_filtlong.fastq.gz`: The length and quality filtered reads in FASTQ from Filtlong
+
+</details>
+
+Trimmed and filtered FASTQ output directories and files will only exist if `--save_porechop_reads` and/or `--save_filtlong_reads` (respectively) are provided to the run command .
+
 No direct host read removal is performed for long reads.
 However, since within this pipeline filtlong uses a read quality based on k-mer matches to the already filtered short reads, reads not overlapping those short reads might be discarded.
 The lower the parameter `--longreads_length_weight`, the higher the impact of the read qualities for filtering.

modules.json

@@ -107,6 +107,11 @@
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
                     },
+                    "filtlong": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "freebayes": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
@@ -203,6 +208,11 @@
                         "git_sha": "3135090b46f308a260fc9d5991d7d2f9c0785309",
                         "installed_by": ["modules"]
                     },
+                    "porechop/abi": {
+                        "branch": "master",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "installed_by": ["modules"]
+                    },
                     "porechop/porechop": {
                         "branch": "master",
                         "git_sha": "1d68c7f248d1a480c5959548a9234602b771199e",