Add samtools to homer/maketagdirectory to use bam files (#1437)

* fix(homer): Update dependancies for maketagdirectory

Closes #1363

* test(homer): Add tests for bam usage

* style(homer): Rename meta test

* fix(homer): Update args order and add missing \\

* docs(homer): Add DESeq2 and edgeR

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* test(homer): Update md5sum

* test(homer): bam => sam

* fix(homer): Use nextflow conda recipe instead of biocontainers with commas

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

modules/homer/maketagdirectory/main.nf

@@ -4,13 +4,13 @@ process HOMER_MAKETAGDIRECTORY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
+    conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
-        'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' :
+        'quay.io/biocontainers/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' }"
 
     input:
-    tuple val(meta), path(bed)
+    tuple val(meta), path(bam)
     path fasta
 
     output:
@@ -26,13 +26,14 @@ process HOMER_MAKETAGDIRECTORY {
     """
     makeTagDirectory \\
         tag_dir \\
+        -genome $fasta \\
         $args \\
-        $bed \\
-        -genome $fasta
+        $bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         homer: $VERSION
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/homer/maketagdirectory/meta.yml

@@ -3,6 +3,8 @@ description: Create a tag directory with the HOMER suite
 keywords:
   - peaks
   - bed
+  - bam
+  - sam
 tools:
   - homer:
       description: |
@@ -10,16 +12,41 @@ tools:
       documentation: http://homer.ucsd.edu/homer/
       doi: 10.1016/j.molcel.2010.05.004.
       licence: ["GPL-3.0-or-later"]
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: hhttp://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+  - DESeq2:
+      description: |
+        Differential gene expression analysis based on the negative binomial distribution
+      homepage: "https://bioconductor.org/packages/DESeq2"
+      documentation: "https://bioconductor.org/packages/DESeq2"
+      tool_dev_url: "https://github.com/mikelove/DESeq2"
+      doi: 10.18129/B9.bioc.DESeq2
+      licence: ["LGPL-3.0-or-later"]
+  - edgeR:
+      description: |
+        Empirical Analysis of Digital Gene Expression Data in R
+      homepage: "https://bioinf.wehi.edu.au/edgeR"
+      documentation: "https://bioconductor.org/packages/edgeR"
+      tool_dev_url: " https://git.bioconductor.org/packages/edgeR"
+      doi: 10.18129/B9.bioc.edgeR
+      licence: ["GPL >=2"]
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bed:
+  - bam:
       type: file
-      description: The peak files in bed format
-      pattern: "*.bed"
+      description: BAM/BED/SAM file
+      pattern: "*.{bam,bed,sam}"
   - fasta:
       type: file
       description: Fasta file of reference genome

tests/modules/homer/maketagdirectory/main.nf

@@ -2,19 +2,22 @@
 
 nextflow.enable.dsl = 2
 
-include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf'
+include {
+    HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BED
+    HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BAM
+} from '../../../../modules/homer/maketagdirectory/main.nf'
 
-workflow test_homer_maketagdirectory {
+workflow test_homer_maketagdirectory_bed {
     input = [[id:'test'],
              [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
               file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    HOMER_MAKETAGDIRECTORY (input, fasta)
+    HOMER_MAKETAGDIRECTORY_BED (input, fasta)
 }
 
 
-workflow test_homer_meta_maketagdirectory {
+workflow test_homer_maketagdirectory_meta {
     input =
         [[[ id:'test1'],
           [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]],
@@ -25,8 +28,14 @@ workflow test_homer_meta_maketagdirectory {
 
     meta_input = [[id: 'meta_test']] + [ input.collect{it[1]}.flatten() ]
 
-    HOMER_MAKETAGDIRECTORY (meta_input, fasta)
+    HOMER_MAKETAGDIRECTORY_BED (meta_input, fasta)
 }
 
-// TODO Make a failing bam test
-// TODO Make a pass bam test that feeds the bam through samtools first
+workflow test_homer_maketagdirectory_bam {
+    input = [[id:'test'],
+             [file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HOMER_MAKETAGDIRECTORY_BAM (input, fasta)
+}

tests/modules/homer/maketagdirectory/nextflow.config

@@ -2,8 +2,12 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: HOMER_MAKETAGDIRECTORY {
+    withName: HOMER_MAKETAGDIRECTORY_BED {
         ext.args = '-format bed'
     }
 
+    withName: HOMER_MAKETAGDIRECTORY_BAM {
+        ext.args = '-format sam'
+    }
+
 }

tests/modules/homer/maketagdirectory/test.yml

@@ -1,5 +1,5 @@
-- name: homer maketagdirectory
-  command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
+- name: homer maketagdirectory bed
+  command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory_bed -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
   tags:
     - homer
     - homer/maketagdirectory
@@ -11,12 +11,12 @@
     - path: output/homer/tag_dir/tagCountDistribution.txt
       md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
     - path: output/homer/tag_dir/tagInfo.txt
-      md5sum: 816baa642c946f8284eaa465638e9abb
+      md5sum: ff56f30411b221b847aa4e6e9a6098a1
     - path: output/homer/tag_dir/tagLengthDistribution.txt
       md5sum: e5aa2b9843ca9c04ace297280aed6af4
 
-- name: homer meta maketagdirectory
-  command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_meta_maketagdirectory -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
+- name: homer maketagdirectory meta
+  command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory_meta -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
   tags:
     - homer
     - homer/maketagdirectory
@@ -28,6 +28,23 @@
     - path: output/homer/tag_dir/tagCountDistribution.txt
       md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
     - path: output/homer/tag_dir/tagInfo.txt
-      md5sum: 816baa642c946f8284eaa465638e9abb
+      md5sum: ff56f30411b221b847aa4e6e9a6098a1
     - path: output/homer/tag_dir/tagLengthDistribution.txt
       md5sum: e5aa2b9843ca9c04ace297280aed6af4
+
+- name: homer maketagdirectory bam
+  command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory_bam -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
+  tags:
+    - homer
+    - homer/maketagdirectory
+  files:
+    - path: output/homer/tag_dir/MT192765.1.tags.tsv
+      md5sum: 365808c4751ef6dd7085ac52037a22bc
+    - path: output/homer/tag_dir/tagAutocorrelation.txt
+      md5sum: 8b396f2aef1cdd3af4fab57b142d3250
+    - path: output/homer/tag_dir/tagCountDistribution.txt
+      md5sum: afc6d007096c3872bbe84c9dc8edb832
+    - path: output/homer/tag_dir/tagInfo.txt
+      md5sum: fbaf46eeb8a0723fa8b5eabd93f9d821
+    - path: output/homer/tag_dir/tagLengthDistribution.txt
+      md5sum: 44f231adb2a705ae81950808c55cf248