Added ability to auto-create samplesheet for nf-core/phageannotator

.github/workflows/ci.yml

@@ -64,6 +64,7 @@ jobs:
             test_virus_identification,
             test_single_end,
             test_concoct,
+            test_generatesamplesheet
           ]
     steps:
       - name: Free some space

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#543](https://github.com/nf-core/mag/pull/543) - Automatic samplesheet generation for nf-core/phageannotator (@CarsonJM)
+
 ### `Changed`
 
 ### `Fixed`

README.md

@@ -36,9 +36,10 @@ The pipeline then:
 - (optionally) performs ancient DNA assembly validation using [PyDamage](https://github.com/maxibor/pydamage) and contig consensus sequence recalling with [Freebayes](https://github.com/freebayes/freebayes) and [BCFtools](http://samtools.github.io/bcftools/bcftools.html)
 - predicts protein-coding genes for the assemblies using [Prodigal](https://github.com/hyattpd/Prodigal), and bins with [Prokka](https://github.com/tseemann/prokka) and optionally [MetaEuk](https://www.google.com/search?channel=fs&client=ubuntu-sn&q=MetaEuk)
 - performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), and/or with [CONCOCT](https://github.com/BinPro/CONCOCT), and checks the quality of the genome bins using [Busco](https://busco.ezlab.org/), or [CheckM](https://ecogenomics.github.io/CheckM/), and optionally [GUNC](https://grp-bork.embl-community.io/gunc/).
-- Performs ancient DNA validation and repair with [pyDamage](https://github.com/maxibor/pydamage) and [freebayes](https://github.com/freebayes/freebayes)
+- performs ancient DNA validation and repair with [pyDamage](https://github.com/maxibor/pydamage) and [freebayes](https://github.com/freebayes/freebayes)
 - optionally refines bins with [DAS Tool](https://github.com/cmks/DAS_Tool)
 - assigns taxonomy to bins using [GTDB-Tk](https://github.com/Ecogenomics/GTDBTk) and/or [CAT](https://github.com/dutilh/CAT) and optionally identifies viruses in assemblies using [geNomad](https://github.com/apcamargo/genomad), or Eukaryotes with [Tiara](https://github.com/ibe-uw/tiara)
+- generates a samplesheet that can be used as input for other nf-core pipelines. Currently, [phageannotator](https://github.com/nf-core/phageannotator) is supported.
 
 Furthermore, the pipeline creates various reports in the results directory specified, including a [MultiQC](https://multiqc.info/) report summarizing some of the findings and software versions.
 

conf/test_generatesamplesheet.config

@@ -0,0 +1,41 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/mag -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    input                           = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.multirun.csv'
+    generate_downstream_samplesheet = 'phageannotator'
+    skip_clipping                   = true
+    skip_adapter_trimming           = true
+    keep_phix                       = true
+    centrifuge_db                   = null
+    kraken2_db                      = null
+    skip_krona                      = true
+    coassemble_group                = true
+    megahit_fix_cpu_1               = true
+    skip_spadeshybrid               = true
+    skip_spades                     = true
+    skip_quast                      = true
+    skip_prodigal                   = true
+    skip_binning                    = true
+    skip_binqc                      = true
+    skip_gtdbtk                     = true
+    skip_prokka                     = true
+}

docs/output.md

@@ -21,6 +21,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Genome annotation of binned genomes](#genome-annotation-of-binned-genomes)
 - [Additional summary for binned genomes](#additional-summary-for-binned-genomes)
 - [Ancient DNA](#ancient-dna)
+- [Samplesheet generation](#sampleseet-generation)
 - [MultiQC](#multiqc) - aggregate report, describing results of the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -706,6 +707,20 @@ Because of aDNA damage, _de novo_ assemblers sometimes struggle to call a correc
 
 </details>
 
+### Samplesheet generation
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `samplesheet/`
+  - `[generate_downstream_samplesheet].csv`: a samplesheet in CSV format that can be directly used as input for the specified nf-core pipeline
+
+</details>
+
+Currently, samplesheets for the following nf-core pipelines can be automatically generated:
+
+- [phageannotator](https://github.com/nf-core/phageannotator): a pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences. Utilizes quality controlled reads and contigs generate by nf-core/mag
+
 ### MultiQC
 
 <details markdown="1">

modules.json

@@ -36,6 +36,11 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "cat/cat": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "cat/fastq": {
                         "branch": "master",
                         "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",