Adding tcoffee module

.github/workflows/tcoffee.yml

@@ -2,7 +2,7 @@ name: FastQC
 on:
   push: {}
   pull_request:
-    paths: tools/fastqc/*
+    paths: tools/tcoffee/*
 
 jobs:
   run_ci_test:
@@ -20,4 +20,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./tools/fastqc/test/ -ansi-log false
+    - run: nextflow run ./tools/tcoffee/test/ -ansi-log false

tools/tcoffee/main.nf

@@ -0,0 +1,18 @@
+process tcoffee {
+    tag {fasta}
+    // publishDir "${params.outdir}/tcoffee" //not working
+    publishDir "${baseDir}/results/tcoffee", mode: 'copy'
+    container 'quay.io/biocontainers/t_coffee:11.0.8--py27pl5.22.0_5'
+
+    input:
+    path(fasta)
+
+    output:
+    path("${fasta}.aln")
+
+    script:
+    """
+    t_coffee -seq $fasta -outfile ${fasta}.aln
+    """
+}
+

tools/tcoffee/meta.yml

@@ -0,0 +1,28 @@
+name: t-coffee
+description: Run tcofee multiple sequence alignment
+keywords:
+    - MSA
+    - sequence aligment
+tools:
+    - t-coffee:
+        description: |
+            T-Coffee is a multiple sequence alignment package.
+            It uses a progressive approach and a consistency objective
+            function for alignment evaluation.
+        homepage: http://www.tcoffee.org/
+        documentation: http://www.tcoffee.org/Projects/tcoffee/index.html#DOCUMENTATION
+input:
+    -
+        - fasta:
+            type: path
+            description: Input fasta file
+            pattern: *.{fasta,fa,tfa}
+output:
+    -
+        - alignment:
+            type: file
+            description: tcoffee alignment file
+            pattern: *.aln
+
+authors:
+    - @JoseEspinosa

tools/tcoffee/test/main.nf

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+include check_output from  '../../../nf-core/module_testing/check_process_outputs.nf'
+include tcoffee from '../main.nf'
+
+// Define input channels
+fasta = Channel.fromPath('../../../test-datasets/tools/tcoffee/input/BBA0001.tfa')
+
+// Run the workflow
+workflow {
+    tcoffee(fasta)
+    // .check_output()
+}
+
+
+
+
+

tools/tcoffee/test/nextflow.config

@@ -0,0 +1,2 @@
+docker.enabled = true
+params.outdir = './results'