Mercurial > repos > kkonganti > cfsan_centriflaken

changeset 97:8d7f482c64de

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"planemo upload"
author kkonganti
date Fri, 29 Jul 2022 11:11:07 -0400
parents ef0b422978fd
children 778b2e98af38
files 0.3.0/README.md 0.3.0/lib/help/megahit.nf 0.3.0/lib/help/spades.nf 0.3.0/modules/megahit/assemble/main.nf 0.3.0/modules/multiqc/main.nf 0.3.0/modules/spades/assemble/main.nf 0.3.0/nextflow.config 0.3.0/readme/centriflaken.md 0.3.0/readme/centriflaken_hy.md 0.3.0/workflows/conf/centriflaken.config 0.3.0/workflows/conf/centriflaken_hy.config
diffstat 11 files changed, 88 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/0.3.0/README.md	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/README.md	Fri Jul 29 11:11:07 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/0.2.1
+module load cpipes/0.3.0
 
 cpipes --pipeline centriflaken [options]
 ```
--- a/0.3.0/lib/help/megahit.nf	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/lib/help/megahit.nf	Fri Jul 29 11:11:07 2022 -0400
@@ -8,6 +8,12 @@
 tool.helpparams = [:]
 
     toolspecs = [
+        'megahit_run': [
+            clihelp: 'Run MEGAHIT assembler. Default: ' +
+                (params.megahit_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
         'megahit_min_count': [
             clihelp: '<int>. Minimum multiplicity for filtering (k_min+1)-mers. ' +
                 "Defaut: ${params.megahit_min_count}",
--- a/0.3.0/lib/help/spades.nf	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/lib/help/spades.nf	Fri Jul 29 11:11:07 2022 -0400
@@ -8,6 +8,12 @@
 tool.helpparams = [:]
 
     toolspecs = [
+        'spades_run': [
+            clihelp: 'Run SPAdes assembler. Default: ' +
+                (params.spades_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
         'spades_isolate': [
             clihelp: 'This flag is highly recommended for high-coverage isolate and ' +
                 "multi-cell data. Defaut: ${params.spades_isolate}",
--- a/0.3.0/modules/megahit/assemble/main.nf	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/modules/megahit/assemble/main.nf	Fri Jul 29 11:11:07 2022 -0400
@@ -1,6 +1,6 @@
 process MEGAHIT_ASSEMBLE {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_higher'
 
     module (params.enable_module ? "${params.swmodulepath}${params.fs}megahit${params.fs}1.2.9" : null)
     conda (params.enable_conda ? "bioconda::megahit=1.2.9" : null)
@@ -54,4 +54,4 @@
         END_VERSIONS
         """
     }
-}
\ No newline at end of file
+}
--- a/0.3.0/modules/multiqc/main.nf	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/modules/multiqc/main.nf	Fri Jul 29 11:11:07 2022 -0400
@@ -15,7 +15,7 @@
     path "*multiqc*"
     path "*multiqc_report.html", emit: report
     path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
+    path "*_plots"             , optional: true, emit: plots
     path "versions.yml"        , emit: versions
 
     when:
--- a/0.3.0/modules/spades/assemble/main.nf	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/modules/spades/assemble/main.nf	Fri Jul 29 11:11:07 2022 -0400
@@ -1,6 +1,6 @@
 process SPADES_ASSEMBLE {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_higher'
 
     module (params.enable_module ? "${params.swmodulepath}${params.fs}spades${params.fs}3.15.3" : null)
     conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null)
--- a/0.3.0/nextflow.config	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/nextflow.config	Fri Jul 29 11:11:07 2022 -0400
@@ -27,8 +27,8 @@
 includeConfig "${pd}${fs}conf${fs}modules.config"
 
 // Nextflow runtime profiles
-conda.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/kondagac_cache'
-singularity.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/cingularitygac_cache'
+conda.cacheDir = '/tool-local-data/cfsan-centriflaken-db/0/kondagac_cache'
+singularity.cacheDir = '/tool-local-data/cfsan-centriflaken-db/0/cingularitygac_cache'
 
 profiles {
     standard {
--- a/0.3.0/readme/centriflaken.md	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/readme/centriflaken.md	Fri Jul 29 11:11:07 2022 -0400
@@ -15,7 +15,7 @@
 #### Workflow Usage
 
 ```bash
-module load cpipes/0.2.1
+module load cpipes/0.3.0
 
 cpipes --pipeline centriflaken [options]
 ```
--- a/0.3.0/readme/centriflaken_hy.md	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/readme/centriflaken_hy.md	Fri Jul 29 11:11:07 2022 -0400
@@ -15,7 +15,7 @@
 #### Workflow Usage
 
 ```bash
-module load cpipes/0.2.1
+module load cpipes/0.3.0
 
 cpipes --pipeline centriflaken_hy [options]
 ```
@@ -43,7 +43,7 @@
 ```text
 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help
 N E X T F L O W  ~  version 21.12.1-edge
-Launching `/nfs/software/apps/cpipes/0.2.1/cpipes` [wise_noyce] - revision: 72db279311
+Launching `/home/Kranti.Konganti/apps/cpipes/cpipes` [condescending_jang] - revision: 72db279311
 ================================================================================
              (o)                  
   ___  _ __   _  _ __    ___  ___ 
@@ -57,7 +57,7 @@
 --------------------------------------------------------------------------------
 Name                            : CPIPES
 Author                          : Kranti.Konganti@fda.hhs.gov
-Version                         : 0.2.1
+Version                         : 0.3.0
 Center                          : CFSAN, FDA.
 ================================================================================
 
@@ -65,7 +65,7 @@
 
 Author                          : Kranti.Konganti@fda.hhs.gov
 
-Version                         : 0.2.0
+Version                         : 0.3.0
 
 
 Usage                           : cpipes --pipeline centriflaken_hy [options]
@@ -176,6 +176,59 @@
 --centrifuge_ignore_quals       : Treat all quality values as 30 on Phred 
                                   scale. Default: false
 
+--megahit_run                   : Run MEGAHIT assembler. Default: true
+
+--megahit_min_count             : <int>. Minimum multiplicity for filtering (
+                                  k_min+1)-mers. Defaut: false
+
+--megahit_k_list                : Comma-separated list of kmer size. All 
+                                  values must be odd, in the range 15-255, 
+                                  increment should be <= 28. Ex: '21,29,39,59,
+                                  79,99,119,141'. Default: false
+
+--megahit_no_mercy              : Do not add mercy k-mers. Default: false
+
+--megahit_bubble_level          : <int>. Intensity of bubble merging (0-2), 0 
+                                  to disable. Default: false
+
+--megahit_merge_level           : <l,s>. Merge complex bubbles of length <= l*
+                                  kmer_size and similarity >= s. Default: 
+                                  false
+
+--megahit_prune_level           : <int>. Strength of low depth pruning (0-3). 
+                                  Default: false
+
+--megahit_prune_depth           : <int>. Remove unitigs with avg k-mer depth 
+                                  less than this value. Default: false
+
+--megahit_low_local_ratio       : <float>. Ratio threshold to define low 
+                                  local coverage contigs. Default: false
+
+--megahit_max_tip_len           : <int>. remove tips less than this value [<
+                                  int> * k]. Default: false
+
+--megahit_no_local              : Disable local assembly. Default: false
+
+--megahit_kmin_1pass            : Use 1pass mode to build SdBG of k_min. 
+                                  Default: false
+
+--megahit_preset                : <str>. Override a group of parameters. 
+                                  Valid values are meta-sensitive which 
+                                  enforces '--min-count 1 --k-list 21,29,39,
+                                  49,...,129,141', meta-large (large & 
+                                  complex metagenomes, like soil) which 
+                                  enforces '--k-min 27 --k-max 127 --k-step 
+                                  10'. Default: meta-sensitive
+
+--megahit_mem_flag              : <int>. SdBG builder memory mode. 0: minimum; 
+                                  1: moderate; 2: use all memory specified. 
+                                  Default: 2
+
+--megahit_min_contig_len        : <int>.  Minimum length of contigs to output. 
+                                  Default: false
+
+--spades_run                    : Run SPAdes assembler. Default: false
+
 --spades_isolate                : This flag is highly recommended for high-
                                   coverage isolate and multi-cell data. 
                                   Defaut: false
@@ -212,7 +265,7 @@
                                   Default: false
 
 --spades_only_assembler         : Runs only the SPAdes assembler module (
-                                  without read error correction).Default: 
+                                  without read error correction). Default: 
                                   false
 
 --spades_careful                : Tries to reduce the number of mismatches 
--- a/0.3.0/workflows/conf/centriflaken.config	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/workflows/conf/centriflaken.config	Fri Jul 29 11:11:07 2022 -0400
@@ -2,13 +2,13 @@
     workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
     workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
     workflow_version = '0.2.0'
-    centrifuge_x = '/tool/tool-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
+    centrifuge_x = '/tool-local-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
     centrifuge_extract_bug = 'Escherichia coli'
     centrifuge_save_aligned = false
     centrifuge_save_unaligned = false
     centrifuge_out_fmt_sam = false
     centrifuge_ignore_quals = false
-    kraken2_db = '/tool/tool-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
+    kraken2_db = '/tool-local-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
     kraken2_confidence = '0.0'
     kraken2_quick = false
     kraken2_use_mpa_style = false
@@ -34,7 +34,7 @@
     ectyper_perc_opcov = 95
     ectyper_perc_hpcov = 50
     serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
-    serotypefinder_db = '/tool/tool-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
+    serotypefinder_db = '/tool-local-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
     serotypefinder_min_cov = 0.80
     serotypefinder_min_threshold = 0.85
     serotypefinder_x = true
@@ -48,10 +48,10 @@
     mlst_mincov = 10
     mlst_minscore = 50
     amrfinderplus_run = false
-    amrfinderplus_db = '/tool/tool-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
+    amrfinderplus_db = '/tool-local-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
     amrfinderplus_genes = true
     abricate_run = true
-    abricate_datadir = '/tool/tool-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
+    abricate_datadir = '/tool-local-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
     abricate_minid = 90
     abricate_mincov = 80
     abricate_summary_run = true
--- a/0.3.0/workflows/conf/centriflaken_hy.config	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/workflows/conf/centriflaken_hy.config	Fri Jul 29 11:11:07 2022 -0400
@@ -2,13 +2,13 @@
     workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
     workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
     workflow_version = '0.3.0'
-    centrifuge_x = '/tool/tool-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
+    centrifuge_x = '/tool-local-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
     centrifuge_extract_bug = 'Escherichia coli'
     centrifuge_save_aligned = false
     centrifuge_save_unaligned = false
     centrifuge_out_fmt_sam = false
     centrifuge_ignore_quals = false
-    kraken2_db = '/tool/tool-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
+    kraken2_db = '/tool-local-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
     kraken2_confidence = '0.0'
     kraken2_quick = false
     kraken2_use_mpa_style = false
@@ -55,7 +55,7 @@
     ectyper_perc_opcov = 95
     ectyper_perc_hpcov = 50
     serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
-    serotypefinder_db = '/tool/tool-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
+    serotypefinder_db = '/tool-local-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
     serotypefinder_min_cov = 0.80
     serotypefinder_min_threshold = 0.85
     serotypefinder_x = true
@@ -69,10 +69,10 @@
     mlst_mincov = 10
     mlst_minscore = 50
     amrfinderplus_run = false
-    amrfinderplus_db = '/tool/tool-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
+    amrfinderplus_db = '/tool-local-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
     amrfinderplus_genes = true
     abricate_run = true
-    abricate_datadir = '/tool/tool-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
+    abricate_datadir = '/tool-local-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
     abricate_minid = 90
     abricate_mincov = 80
     abricate_summary_run = true