Changed Cutadapt to use nf-core modules

.github/workflows/ci.yml

@@ -111,6 +111,7 @@ jobs:
           - "--skip_plasmidid false --skip_asciigenome"
           - "--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz"
           - "--bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz"
+          - "--skip_noninternal_primers --threeprime_adapters"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev

CHANGELOG.md

@@ -28,20 +28,23 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR #434](https://github.com/nf-core/viralrecon/pull/434)] - Add blast result filtering through `min_contig_length` and `min_perc_contig_aligned`.
 - [[PR #438](https://github.com/nf-core/viralrecon/pull/438)] - Update fastp container to 0.23.4
 - [[PR #439](https://github.com/nf-core/viralrecon/pull/439)] - Fix cardinality issue when using `--bowtie2_index`
+- [[PR #435](https://github.com/nf-core/viralrecon/pull/435)] - Changed to a patched cutadapt from nf-core modules, added `skip_noninternal_primers` param to allow users to process primers inside the pipeline, and added `threeprime_adapters` to determine whether primers are 3' or 5' adapters.
 
 ### Parameters
 
-| Old parameter | New parameter               |
-| ------------- | --------------------------- |
-|               | `--skip_freyja`             |
-|               | `--freyja_repeats`          |
-|               | `--freyja_db_name`          |
-|               | `--freyja_barcodes`         |
-|               | `--freyja_lineages`         |
-|               | `--skip_freyja_boot`        |
-|               | `--additional_annotation`   |
-|               | `--min_contig_length`       |
-|               | `--min_perc_contig_aligned` |
+| Old parameter | New parameter                |
+| ------------- | ---------------------------- |
+|               | `--skip_freyja`              |
+|               | `--freyja_repeats`           |
+|               | `--freyja_db_name`           |
+|               | `--freyja_barcodes`          |
+|               | `--freyja_lineages`          |
+|               | `--skip_freyja_boot`         |
+|               | `--additional_annotation`    |
+|               | `--min_contig_length`        |
+|               | `--min_perc_contig_aligned`  |
+|               | `--skip_noninternal_primers` |
+|               | `--threeprime_adapters`      |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.
@@ -53,9 +56,10 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
+| `cutadapt` |             | 4.6         |
+| `fastp`    | 0.23.2      | 0.23.4      |
 | `freyja`   |             | 1.5.0       |
 | `multiqc`  | 1.14        | 1.19        |
-| `fastp`    | 0.23.2      | 0.23.4      |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >

conf/modules_illumina.config

@@ -757,7 +757,14 @@ if (!params.skip_assembly) {
                     enabled: params.save_reference
                 ]
             }
-
+            withName: 'PREPARE_PRIMER_FASTA' {
+                ext.args = '^'
+                ext.prefix = { "${meta.id}"}
+                publishDir = [
+                    path: { "${params.outdir}/assembly/cutadapt/log" },
+                    enabled: false
+                ]
+            }
             withName: 'CUTADAPT' {
                 ext.args = '--overlap 5 --minimum-length 30 --error-rate 0.1'
                 ext.prefix = { "${meta.id}.primer_trim" }

docs/usage.md

@@ -321,6 +321,20 @@ To learn how to provide additional arguments to a particular tool of the pipelin
 
 [Freyja](https://github.com/andersen-lab/Freyja) relies on a dataset of barcodes that use lineage defining mutations (see [UShER](https://usher-wiki.readthedocs.io/en/latest/#)). By default the most recent barcodes will be downloaded and used. However, if analyses need to be compared across multiple datasets, it might be of interest to re-use the same barcodes, or to rerun all Freyja analyses with the most recent dataset. To do this, specify the barcodes and lineages using the `--freyja_barcodes`, `--freyja_lineages` parameters, respectivly. The boostrapping of Freyja can be skipped by specifying `--skip_freyja_boot`.
 
+### Cutadapt
+
+According to [Cutadapt's documentation regarding adapter types](https://cutadapt.readthedocs.io/en/stable/guide.html#adapter-types), you can have:
+
+- Regular 3’ adapter: `-a ADAPTER`
+  - Set `--skip_noninternal_primers` to `true`
+  - Set `--threeprime_adapters` to `true`
+- Regular 5’ adapter: `-g ADAPTER`
+  - Set `--skip_noninternal_primers` to `true`
+- Non-internal 3’ adapter: `-a ADAPTERX`:
+  - Change `modules_illumina.config` > `PREPARE_PRIMER_FASTA` > `ext.args` to use `$` instead of `^` to add the X at the end of the sequence.
+  - Set `--threeprime_adapters` to `true`
+- **Non-internal 5’ adapter**: `-g XADAPTER`: **This is the option by default**.
+
 ### nf-core/configs
 
 In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.

modules.json

@@ -105,6 +105,11 @@
                         "git_sha": "1b0ffa4e5aed5b7e3cd4311af31bd3b2c8345051",
                         "installed_by": ["modules"]
                     },
+                    "cutadapt": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",

modules/local/prepare_primer_fasta.nf

@@ -0,0 +1,30 @@
+process PREPARE_PRIMER_FASTA {
+    tag "$adapters"
+    label 'process_low'
+
+    conda "conda-forge::sed=4.7"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
+
+    input:
+    path adapters
+
+    output:
+    path 'adapters.sub.fa', emit: adapters
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    sed -r '/^[ACTGactg]+\$/ s/$args/X/g' $adapters > adapters.sub.fa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
+    END_VERSIONS
+    """
+}