Remove unused modules (bowtie2/build, fastqscreen/buildfromindex)

CHANGELOG.md

@@ -82,6 +82,8 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#174](https://github.com/nf-core/seqinspector/pull/174) No params included in workflows
 - [#175](https://github.com/nf-core/seqinspector/pull/175) Update all modules and migrate the whole pipeline to using topic versions
 - [#176](https://github.com/nf-core/seqinspector/pull/176) No modules binaries
+- [#177](https://github.com/nf-core/seqinspector/pull/177) Remove non used modules
+- [#177](https://github.com/nf-core/seqinspector/pull/177) Move PREPARE_GENOME to the root main.nf script
 
 ### `Dependencies`
 

CITATIONS.md

@@ -10,10 +10,6 @@
 
 ## Pipeline tools
 
-- [Bowtie2](https://www.nature.com/articles/nmeth.1923)
-
-  > Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Apr;9(4):357-9. doi: 10.1038/nmeth.1923. PubMed PMID: 22388286.
-
 - [BWAMEM2](https://ieeexplore.ieee.org/abstract/document/8820962)
 
   > Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041

README.md

@@ -54,7 +54,6 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 
 | Tool        | Version |
 | ----------- | ------- |
-| bowtie2     | 2.5.4   |
 | bwamem2     | 2.3     |
 | fastqc      | 0.12.1  |
 | fastqscreen | 0.16.0  |

conf/base.config

@@ -9,9 +9,9 @@
 */
 
 process {
-    cpus   = { 1      * task.attempt }
-    memory = { 6.GB   * task.attempt }
-    time   = { 4.h    * task.attempt }
+    cpus          = { 1 * task.attempt }
+    memory        = { 6.GB * task.attempt }
+    time          = { 4.h * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -23,36 +23,36 @@ process {
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
-    withLabel:process_single {
-        cpus   = { 1                   }
+    withLabel: process_single {
+        cpus   = { 1 }
         memory = { 6.GB * task.attempt }
-        time   = { 4.h  * task.attempt }
+        time   = { 4.h * task.attempt }
     }
-    withLabel:process_low {
-        cpus   = { 2     * task.attempt }
+    withLabel: process_low {
+        cpus   = { 2 * task.attempt }
         memory = { 12.GB * task.attempt }
-        time   = { 4.h   * task.attempt }
+        time   = { 4.h * task.attempt }
     }
-    withLabel:process_medium {
-        cpus   = { 6     * task.attempt }
+    withLabel: process_medium {
+        cpus   = { 6 * task.attempt }
         memory = { 36.GB * task.attempt }
-        time   = { 8.h   * task.attempt }
+        time   = { 8.h * task.attempt }
     }
-    withLabel:process_high {
-        cpus   = { 12    * task.attempt }
+    withLabel: process_high {
+        cpus   = { 12 * task.attempt }
         memory = { 72.GB * task.attempt }
-        time   = { 16.h  * task.attempt }
+        time   = { 16.h * task.attempt }
     }
-    withLabel:process_long {
-        time   = { 20.h  * task.attempt }
+    withLabel: process_long {
+        time = { 20.h * task.attempt }
     }
-    withLabel:process_high_memory {
+    withLabel: process_high_memory {
         memory = { 200.GB * task.attempt }
     }
-    withLabel:error_ignore {
+    withLabel: error_ignore {
         errorStrategy = 'ignore'
     }
-    withLabel:error_retry {
+    withLabel: error_retry {
         errorStrategy = 'retry'
         maxRetries    = 2
     }

conf/modules.config

@@ -11,21 +11,20 @@
 */
 
 process {
-
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         mode: params.publish_dir_mode
     ]
 
-    withName: 'SEQTK_SAMPLE' {
+    withName: SEQTK_SAMPLE {
         ext.args = '-s100'
     }
 
-    withName: 'FASTQC' {
+    withName: FASTQC {
         ext.args = '--quiet'
     }
 
-    withName: 'SEQFU_STATS' {
+    withName: SEQFU_STATS {
         ext.args   = ''
         publishDir = [
             path: { "${params.outdir}/seqfu_stats" },
@@ -34,93 +33,94 @@ process {
         ]
     }
 
-    withName: 'BWAMEM2_INDEX' {
+    withName: BWAMEM2_INDEX {
         publishDir = [
             path: { "${params.outdir}/bwamem2_index" },
             mode: params.publish_dir_mode
         ]
     }
 
-        withName: 'PICARD_CREATESEQUENCEDICTIONARY' {
+    withName: PICARD_CREATESEQUENCEDICTIONARY {
         publishDir = [
             path: { "${params.outdir}/picard_createsequencedictionary" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'BWAMEM2_MEM' {
+    withName: BWAMEM2_MEM {
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
+    withName: PICARD_COLLECTMULTIPLEMETRICS {
         publishDir = [
             path: { "${params.outdir}/picard_collectmultiplemetrics" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'PICARD_COLLECTHSMETRICS' {
+    withName: PICARD_COLLECTHSMETRICS {
+        ext.args   = { "--TMP_DIR ." }
         publishDir = [
             path: { "${params.outdir}/picard_collecthsmetrics" },
             mode: params.publish_dir_mode
         ]
-        ext.args = {"--TMP_DIR ."}
     }
 
-    withName: 'SAMTOOLS_FAIDX' {
+    withName: SAMTOOLS_FAIDX {
         publishDir = [
             path: { "${params.outdir}/samtools_faidx" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'SAMTOOLS_INDEX' {
+    withName: SAMTOOLS_INDEX {
         publishDir = [
             path: { "${params.outdir}/bwamem2_mem" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'RUNDIRPARSER' {
-        publishDir = [
-            path: { "${params.outdir}/rundirparser" },
-            mode: params.publish_dir_mode,
+    withName: RUNDIRPARSER {
             // The process _mqc.txt outputs should have identical names for the same sequencing platforms
             // in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness
             // to avoid overwriting results in the publishDir.
-            saveAs: { filename -> "${meta.dirname}_${filename}" }
-        ]
+            publishDir = [
+            path: { "${params.outdir}/rundirparser" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> "${meta.dirname}_${filename}" }]
     }
 
-    withName: 'MULTIQC_GLOBAL' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+    withName: MULTIQC_GLOBAL {
+        ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc/global_report" },
             mode: params.publish_dir_mode
         ]
     }
 
-    withName: 'MULTIQC_PER_TAG' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+    withName: MULTIQC_PER_TAG {
+        ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc/group_reports" },
             mode: params.publish_dir_mode,
             saveAs: { filename ->
-                if (filename == 'versions.yml') {
-                    return null
-                } else if (filename  =~/\[TAG:.+\]_multiqc_(report\.html|plots|data)/) {
-                        def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
-                        def new_filename = filename.replaceFirst(
-                            "(?<prefix>.*)\\[TAG:${tag}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
-                            '${prefix}${suffix}')
-                    return "${tag}/${new_filename}"
-                } else {
-                    return filename
-                }
+            if (filename == 'versions.yml') {
+                return null
             }
-        ]
+            else if (filename =~ /\[TAG:.+\]_multiqc_(report\.html|plots|data)/) {
+                def tag = (filename =~ /\[TAG:(.+)\]_multiqc_(report\.html|plots|data)/)[0][1]
+                def new_filename = filename.replaceFirst(
+                    "(?<prefix>.*)\\[TAG:${tag}\\]_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                    '${prefix}${suffix}',
+                )
+                return "${tag}/${new_filename}"
+            }
+            else {
+                return filename
+            }
+        }]
     }
 }

conf/test.config

@@ -15,11 +15,11 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
-    fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"
+    input                      = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
+    fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // Genome references
-    genome = 'R64-1-1'
+    genome                     = 'R64-1-1'
 }
 
 process {
@@ -28,5 +28,4 @@ process {
         memory: '8.GB',
         time: '1.h'
     ]
-
 }

conf/test_full.config

@@ -16,8 +16,8 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = params.pipelines_testdata_base_path + 'seqinspector/full_tests/SampleSheet.csv'
+    input                      = params.pipelines_testdata_base_path + 'seqinspector/full_tests/SampleSheet.csv'
 
     // Genome references
-    genome = 'R64-1-1'
+    genome                     = 'R64-1-1'
 }