add module for panaroo, fix pirate tests (#1444)

* add module for panaroo

* update pirate test yaml

* update panaroo test yaml

* update pirate test yaml md5s

* Update main.nf

* Update main.nf

* pin bioperl version

modules/panaroo/run/main.nf

@@ -0,0 +1,36 @@
+process PANAROO_RUN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::panaroo=1.2.9" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/panaroo:1.2.9--pyhdfd78af_0':
+        'quay.io/biocontainers/panaroo:1.2.9--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(gff)
+
+    output:
+    tuple val(meta), path("results/*")                                      , emit: results
+    tuple val(meta), path("results/core_gene_alignment.aln"), optional: true, emit: aln
+    path "versions.yml"                                                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    panaroo \\
+        $args \\
+        -t $task.cpus \\
+        -o results \\
+        -i $gff
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        panaroo: \$(echo \$(panaroo --version 2>&1) | sed 's/^.*panaroo //' ))
+    END_VERSIONS
+    """
+}

modules/panaroo/run/meta.yml

@@ -0,0 +1,47 @@
+name: "panaroo_run"
+description: A fast and scalable tool for bacterial pangenome analysis
+keywords:
+  - gff
+  - pan-genome
+  - alignment
+tools:
+  - "panaroo":
+      description: "panaroo - an updated pipeline for pangenome investigation"
+      homepage: "https://gtonkinhill.github.io/panaroo/#/"
+      documentation: "https://gtonkinhill.github.io/panaroo/#/gettingstarted/quickstart"
+      tool_dev_url: "https://github.com/gtonkinhill/panaroo"
+      doi: "10.1186/s13059-020-02090-4"
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - gff:
+      type: file
+      description: A set of GFF3 formatted files
+      pattern: "*.{gff}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - results:
+      type: directory
+      description: Directory containing Panaroo result files
+      pattern: "*/*"
+  - aln:
+      type: file
+      description: Core-genome alignment produced by Panaroo (Optional)
+      pattern: "*.{fasta}"
+
+authors:
+  - "@rpetit3"

modules/pirate/main.nf

@@ -2,10 +2,10 @@ process PIRATE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::pirate=1.0.4" : null)
+    conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_1' :
-        'quay.io/biocontainers/pirate:1.0.4--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_2' :
+        'quay.io/biocontainers/pirate:1.0.4--hdfd78af_2' }"
 
     input:
     tuple val(meta), path(gff)

tests/config/pytest_modules.yml

@@ -1248,6 +1248,10 @@ pairtools/sort:
   - modules/pairtools/sort/**
   - tests/modules/pairtools/sort/**
 
+panaroo/run:
+  - modules/panaroo/run/**
+  - tests/modules/panaroo/run/**
+
 pangolin:
   - modules/pangolin/**
   - tests/modules/pangolin/**

tests/modules/panaroo/run/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PANAROO_RUN } from '../../../../modules/panaroo/run/main.nf'
+
+workflow test_panaroo_run {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test1_gff'], checkIfExists: true),
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test2_gff'], checkIfExists: true),
+            file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
+        ]
+    ]
+
+    PANAROO_RUN ( input )
+}

tests/modules/panaroo/run/nextflow.config

@@ -0,0 +1,8 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: PANAROO_RUN {
+        ext.args = '--clean-mode strict -a core'
+    }
+}

tests/modules/panaroo/run/test.yml

@@ -0,0 +1,38 @@
+- name: panaroo run test_panaroo_run
+  command: nextflow run tests/modules/panaroo/run -entry test_panaroo_run -c tests/config/nextflow.config
+  tags:
+    - panaroo/run
+    - panaroo
+  files:
+    - path: output/panaroo/results/combined_DNA_CDS.fasta
+      md5sum: 92bd4f6b9c84c84c0989d77d2558b7d1
+    - path: output/panaroo/results/combined_protein_CDS.fasta
+      md5sum: 7a5636c4f2abc190f5dd4dfbb1da7034
+    - path: output/panaroo/results/combined_protein_cdhit_out.txt
+      md5sum: 2164b81606712b53af2198b4d50eed08
+    - path: output/panaroo/results/combined_protein_cdhit_out.txt.clstr
+      md5sum: aaa9fc2b797c932b6d9ff2df640113f1
+    - path: output/panaroo/results/core_alignment_header.embl
+      contains: ["DNA", "feature", "locus_tag"]
+    - path: output/panaroo/results/core_gene_alignment.aln
+      contains: ["test1", "test2", "test3"]
+    - path: output/panaroo/results/final_graph.gml
+      contains: ["graph", "isolateNames", "test3"]
+    - path: output/panaroo/results/gene_data.csv
+      md5sum: 45df2d26ac81754b858c0e4757e834b2
+    - path: output/panaroo/results/gene_presence_absence.Rtab
+      md5sum: 9efbed5df121dc0c4fbb58869b65c3e4
+    - path: output/panaroo/results/gene_presence_absence.csv
+      contains: ["Gene", "unique", "test3"]
+    - path: output/panaroo/results/gene_presence_absence_roary.csv
+      contains: ["Gene", "Max", "Fragment"]
+    - path: output/panaroo/results/pan_genome_reference.fa
+      md5sum: d0b03cdfaab8965d86cb1045db3c2d20
+    - path: output/panaroo/results/pre_filt_graph.gml
+      contains: ["graph", "node", "id"]
+    - path: output/panaroo/results/struct_presence_absence.Rtab
+      md5sum: 246017db1175f9b1683dfe60cb2e9b5b
+    - path: output/panaroo/results/summary_statistics.txt
+      md5sum: 9c73c416e1758bea06c67b4ec9fd0720
+    - path: output/panaroo/versions.yml
+      md5sum: 909e7b046a8a87319986d34b7328641c

tests/modules/pirate/main.nf

@@ -14,10 +14,6 @@ workflow test_pirate {
             file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
         ]
     ]
-    //           [ file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000292685.gff", checkIfExists: true),
-    //             file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000298385.gff", checkIfExists: true),
-    //             file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_002849995.gff", checkIfExists: true) ]
-    // ]
 
     PIRATE ( input )
 }

tests/modules/pirate/test.yml

@@ -16,35 +16,35 @@
     - path: output/pirate/results/PIRATE.unique_alleles.tsv
       contains: ["allele_name"]
     - path: output/pirate/results/binary_presence_absence.fasta
-      contains: ["GCF_000292685"]
+      contains: ["test1"]
     - path: output/pirate/results/binary_presence_absence.nwk
-      md5sum: 5b5d86bf97d97de37bb9db514abb7762
+      md5sum: 1fcf7434911bbab39b74791259f1f989
     - path: output/pirate/results/cluster_alleles.tab
       contains: ["g0001"]
-    - path: output/pirate/results/co-ords/GCF_000292685.co-ords.tab
-      md5sum: d5ca0f06ca7ea1f5486683d5859bc9b8
-    - path: output/pirate/results/co-ords/GCF_000298385.co-ords.tab
-      md5sum: a24d6048b3074242bb558c7fa27a8b03
-    - path: output/pirate/results/co-ords/GCF_002849995.co-ords.tab
-      md5sum: 0c08228585f4fa95686e9b025e0fe9c1
+    - path: output/pirate/results/co-ords/test1.co-ords.tab
+      md5sum: f1e75c045b35bae260dadb1a2f000dfa
+    - path: output/pirate/results/co-ords/test2.co-ords.tab
+      md5sum: 953b0d2f1dfd4c3a6a6dd246c9174703
+    - path: output/pirate/results/co-ords/test3.co-ords.tab
+      md5sum: 61f2c52ef77dc9a97a200c57b89b7d69
     - path: output/pirate/results/genome2loci.tab
-      md5sum: bbcea5bfcdcafe14a9aa7261c8e931b8
+      md5sum: 2d9cdefd5b1a7f5e20b0a70a6e5fa588
     - path: output/pirate/results/genome_list.txt
-      md5sum: 6534b1635c258ad92b829077addc1ff5
+      md5sum: c19ac63da7949b15179f42093cbf95b8
     - path: output/pirate/results/link_clusters.log
       contains: ["parsing paralog file"]
     - path: output/pirate/results/loci_list.tab
-      contains: ["GCF_000298385_00242"]
+      contains: ["test1_00242"]
     - path: output/pirate/results/loci_paralog_categories.tab
-      md5sum: 6404d2a32526a398f42d7da768a389bd
-    - path: output/pirate/results/modified_gffs/GCF_000292685.gff
-      md5sum: 2b73bda2f84dc634303dc90e641040ca
-    - path: output/pirate/results/modified_gffs/GCF_000298385.gff
-      md5sum: b1a9d6557d47e09249f08a7acdbbd618
-    - path: output/pirate/results/modified_gffs/GCF_002849995.gff
-      md5sum: 68532fc9bb639e6d83c731a069f60cf8
+      md5sum: f8c3d31f445c3cb66bd95ba77be0a7b8
+    - path: output/pirate/results/modified_gffs/test1.gff
+      md5sum: 5dc220e472165c3b693e1017f38fc0e3
+    - path: output/pirate/results/modified_gffs/test2.gff
+      md5sum: 975f5c7fb363caf1be9c53e5e237bb5d
+    - path: output/pirate/results/modified_gffs/test3.gff
+      md5sum: a4735a5ac75ce82aadba8a3de6cabc2e
     - path: output/pirate/results/pan_sequences.fasta
-      md5sum: ed835c77fdb20c36aa9d5208eb7ca0cb
+      md5sum: 0492833706f0f969b49a3555c16ec40d
     - path: output/pirate/results/pangenome.connected_blocks.tsv
       contains: ["block_number"]
     - path: output/pirate/results/pangenome.edges
@@ -59,29 +59,29 @@
       contains: ["g0091"]
     - path: output/pirate/results/pangenome.temp
     - path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated
-      contains: ["GCF_000298385_00242"]
+      contains: ["test1_00242"]
     - path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
-      contains: ["GCF_000298385_00242"]
+      contains: ["test1_00242"]
     - path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
-      contains: ["GCF_000298385_00242"]
+      contains: ["test1_00242"]
     - path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
-      contains: ["GCF_000298385_00242"]
+      contains: ["test1_00242"]
     - path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
-      contains: ["GCF_000298385_00242"]
+      contains: ["test1_00242"]
     - path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
-      contains: ["GCF_000298385_00242"]
+      contains: ["test1_00242"]
     - path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
-      contains: ["GCF_000298385_00242"]
+      contains: ["test1_00242"]
     - path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
-      md5sum: 9da25d27684bfcc5488987ab2d1fd3a1
+      md5sum: ffb3b5bf1ba24bf2bd0be677500139a2
     - path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
-      contains: ["GCF_000298385_00081"]
+      contains: ["test1_00081"]
     - path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
-      contains: ["GCF_000298385_00242"]
+      contains: ["test1_00242"]
     - path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt
       contains: ["chaos"]
     - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta
-      md5sum: 84668b6c65b57026a17a50b0edd02541
+      md5sum: 6e483c773ed90bd50b33f2bd569343e4
     - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb
     - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pot
     - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf
@@ -95,4 +95,4 @@
     - path: output/pirate/results/representative_sequences.ffn
       contains: ["representative_genome"]
     - path: output/pirate/results/split_groups.log
-      contains: ["g0213"]
+      contains: ["g0"]