Mercurial > repos > kkonganti > cfsan_centriflaken

changeset 104:17890124001d

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"planemo upload"
author kkonganti
date Sun, 28 Aug 2022 00:37:10 -0400
parents 96a34c382154
children 52045ea4679d
files 0.4.0/README.md 0.4.0/bin/fastq_dir_to_samplesheet.py 0.4.0/modules/cat/tables/main.nf 0.4.0/modules/centrifuge/process/main.nf 0.4.0/modules/custom/dump_software_versions/main.nf 0.4.0/modules/kraken2/classify/README.md 0.4.0/modules/kraken2/classify/main.nf 0.4.0/modules/kraken2/extract_contigs/main.nf 0.4.0/nextflow.config 0.4.0/readme/centriflaken.md 0.4.0/workflows/centriflaken.nf 0.4.0/workflows/conf/centriflaken.config
diffstat 12 files changed, 42 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/0.4.0/README.md	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/README.md	Sun Aug 28 00:37:10 2022 -0400
@@ -20,7 +20,7 @@
 Following is the example of how to run the `centriflaken` pipeline on the **CFSAN** raven cluster.
 
 ```bash
-module load cpipes/0.3.0
+module load cpipes/0.4.0
 
 cpipes --pipeline centriflaken [options]
 ```
--- a/0.4.0/bin/fastq_dir_to_samplesheet.py	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/bin/fastq_dir_to_samplesheet.py	Sun Aug 28 00:37:10 2022 -0400
@@ -106,7 +106,7 @@
         abs_fq_files = glob.glob(os.path.join(fastq_dir, f"**", f"*{extension}"), recursive=True)
         return sorted(
             [
-                fq for _, fq in enumerate(abs_fq_files) if re.match('^((?!undetermined|unclassified|fail|class|qc|downloads).)*$', fq, flags=re.IGNORECASE)
+                fq for _, fq in enumerate(abs_fq_files) if re.match('^((?!undetermined|unclassified|downloads).)*$', fq, flags=re.IGNORECASE)
             ]
         )
 
--- a/0.4.0/modules/cat/tables/main.nf	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/modules/cat/tables/main.nf	Sun Aug 28 00:37:10 2022 -0400
@@ -47,16 +47,8 @@
         python: \$( python --version | sed 's/Python //g' )
     END_VERSIONS
 
-    headver=""
-    tailver=""
-
-    if [ "${workflow.containerEngine}" != "null" ]; then
-        headver=\$( head --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
-        tailver="\$headver"
-    else
-        headver=\$( head --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
-        tailver=\$( tail --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
-    fi
+    headver=\$( head --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
+    tailver=\$( tail --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
 
     cat <<-END_VERSIONS >> versions.yml
         head: \$headver
--- a/0.4.0/modules/centrifuge/process/main.nf	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/modules/centrifuge/process/main.nf	Sun Aug 28 00:37:10 2022 -0400
@@ -5,7 +5,7 @@
     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
     conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pandas conda-forge::biopython" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' :
         'quay.io/biocontainers/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' }"
 
     input:
--- a/0.4.0/modules/custom/dump_software_versions/main.nf	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/modules/custom/dump_software_versions/main.nf	Sun Aug 28 00:37:10 2022 -0400
@@ -6,8 +6,8 @@
     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
     conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pyyaml" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-ca258a039fcd88610bc4e297b13703e8be53f5ca:d638c4f85566099ea0c74bc8fddc6f531fe56753-0' :
+        'quay.io/biocontainers/mulled-v2-ca258a039fcd88610bc4e297b13703e8be53f5ca:d638c4f85566099ea0c74bc8fddc6f531fe56753-0' }"
 
     input:
     path versions
--- a/0.4.0/modules/kraken2/classify/README.md	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/modules/kraken2/classify/README.md	Sun Aug 28 00:37:10 2022 -0400
@@ -17,7 +17,7 @@
 
 Type: `tuple`
 
-Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
+Takes in the following tuple of metadata (`meta`) and a list of reads or FASTA assembly of type `path` (`reads`) per sample (`id:`).
 
 Ex:
 
@@ -26,7 +26,9 @@
     [ id: 'FAL00870',
        strandedness: 'unstranded',
        single_end: true,
+       is_assembly: false,
        centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
+       kraken2_db: '/hpc/db/kraken2/standard-210914',
     ],
     '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
 ]
@@ -39,7 +41,7 @@
 
 Type: Groovy Map
 
-A Groovy Map containing the metadata about the FASTQ file.
+A Groovy Map containing the metadata about the FASTQ / FASTA file.
 
 Ex:
 
@@ -48,6 +50,7 @@
     id: 'FAL00870',
     strandedness: 'unstranded',
     single_end: true,
+    is_assembly: false,
     kraken2_db: '/hpc/db/kraken2/standard-210914'
 ]
 ```
--- a/0.4.0/modules/kraken2/classify/main.nf	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/modules/kraken2/classify/main.nf	Sun Aug 28 00:37:10 2022 -0400
@@ -19,7 +19,7 @@
     path "versions.yml"                    , emit: versions
 
     when:
-    task.ext.when == null || task.ext.when || reads
+    (task.ext.when == null || task.ext.when) && (meta.is_assembly ? reads.size() : 1)
 
     script:
     def args = task.ext.args ?: ''
--- a/0.4.0/modules/kraken2/extract_contigs/main.nf	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/modules/kraken2/extract_contigs/main.nf	Sun Aug 28 00:37:10 2022 -0400
@@ -5,7 +5,7 @@
     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
     conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pandas conda-forge::biopython" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' :
         'quay.io/biocontainers/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' }"
 
     input:
--- a/0.4.0/nextflow.config	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/nextflow.config	Sun Aug 28 00:37:10 2022 -0400
@@ -22,7 +22,7 @@
     }
 }
 
-// Include modules' conig last.
+// Include modules' config last.
 includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
 includeConfig "${pd}${fs}conf${fs}modules.config"
 
@@ -55,6 +55,7 @@
         params.enable_conda = false
         params.enable_module = false
         singularity.enabled = true
+        singularity.autoMounts = true
         docker.enabled = false
     }
 
@@ -82,6 +83,19 @@
         clusterOptions = '--signal B:USR2'
     }
 
+    eprodcingularity {
+        process.executor = 'slurm'
+        process.queue = 'lowmem,midmem,bigmem'
+        process.memory = '10GB'
+        process.cpus = 4
+        params.enable_conda = false
+        params.enable_module = false
+        singularity.enabled = true
+        singularity.autoMounts = true
+        docker.enabled = false
+        clusterOptions = '--signal B:USR2'
+    }
+
     cingularity {
         process.executor = 'slurm'
         process.queue = 'prod'
--- a/0.4.0/readme/centriflaken.md	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/readme/centriflaken.md	Sun Aug 28 00:37:10 2022 -0400
@@ -15,7 +15,7 @@
 #### Workflow Usage
 
 ```bash
-module load cpipes/0.3.0
+module load cpipes/0.4.0
 
 cpipes --pipeline centriflaken [options]
 ```
@@ -43,7 +43,7 @@
 ```text
 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken --help
 N E X T F L O W  ~  version 21.12.1-edge
-Launching `/nfs/software/apps/cpipes/0.2.1/cpipes` [drunk_ptolemy] - revision: 72db279311
+Launching `/nfs/software/apps/cpipes/0.4.0/cpipes` [crazy_euler] - revision: 72db279311
 ================================================================================
              (o)                  
   ___  _ __   _  _ __    ___  ___ 
@@ -57,7 +57,7 @@
 --------------------------------------------------------------------------------
 Name                            : CPIPES
 Author                          : Kranti.Konganti@fda.hhs.gov
-Version                         : 0.2.1
+Version                         : 0.4.0
 Center                          : CFSAN, FDA.
 ================================================================================
 
@@ -65,7 +65,7 @@
 
 Author                          : Kranti.Konganti@fda.hhs.gov
 
-Version                         : 0.2.0
+Version                         : 0.2.1
 
 
 Usage                           : cpipes --pipeline centriflaken [options]
--- a/0.4.0/workflows/centriflaken.nf	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/workflows/centriflaken.nf	Sun Aug 28 00:37:10 2022 -0400
@@ -126,6 +126,14 @@
             .assembly
             .set { ch_flye_assembly }
 
+        ch_flye_assembly
+            .map {
+                meta, fastq ->
+                meta.is_assembly = true
+                [meta, fastq]
+            }
+            .set { ch_flye_assembly }
+
         ch_flye_assembly.ifEmpty { [ false, false ] }
 
         KRAKEN2_CLASSIFY ( ch_flye_assembly )
--- a/0.4.0/workflows/conf/centriflaken.config	Thu Aug 04 10:58:46 2022 -0400
+++ b/0.4.0/workflows/conf/centriflaken.config	Sun Aug 28 00:37:10 2022 -0400
@@ -1,7 +1,7 @@
 params {
     workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
     workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
-    workflow_version = '0.2.0'
+    workflow_version = '0.2.1'
     centrifuge_x = '/tool-local-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
     centrifuge_extract_bug = 'Escherichia coli'
     centrifuge_save_aligned = false