change publishdir to copy; update changelog; conda env specifics

Author: sateeshperi

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0 [] - [03/25/2022]
+## v1.0 Espresso Myconaut - [03/25/2022]
 
 Initial release of CDCgov/mycosnp-nf, created with the [nf-core](https://nf-co.re/) template.
 
@@ -27,8 +27,8 @@ Initial release of CDCgov/mycosnp-nf, created with the [nf-core](https://nf-co.r
 *   nf-core
 ### `Deprecated`
 
+*   GeneFlow support
 *   QC pdf report
-
 ### `TODO`
 
 *   Intermediate file cleanup and management

conf/base.config

@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
@@ -24,25 +23,24 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_low {
         cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 24.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 24.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_high {
-        cpus   = { check_max( 2    * task.attempt, 'cpus'    ) }
+        cpus   = { check_max( 4    * task.attempt, 'cpus'    ) }
         memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        time   = { check_max( 48.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { check_max( 72.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_high_memory {
         memory = { check_max( 64.GB * task.attempt, 'memory' ) }
@@ -52,7 +50,7 @@ process {
     }
     withLabel:error_retry {
         errorStrategy = 'retry'
-        maxRetries    = 2
+        maxRetries    = 3
     }
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false

docs/usage.md

@@ -23,7 +23,7 @@
 *   Alternatively, you can install nextflow and other dependencies via conda like so:
 
 ```console
-conda create -n nextflow -c bioconda -c conda-forge nf-core nextflow git graphviz
+conda create -n nextflow -c bioconda -c conda-forge nf-core=2.2 nextflow=21.10.6 git=2.35.0 openjdk=8.0312 graphviz
 conda activate nextflow
 ```
 

nextflow.config

@@ -39,7 +39,6 @@ params {
 
     // Config options
     custom_config_version      = 'master'
-    // TODO - add hpc config profiles
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_description = null
     config_profile_contact     = null
@@ -62,7 +61,7 @@ params {
     vcftools_filter            = '--min_GQ "50" --keep_GQ_0_refs --min_percent_alt_in_AD "0.8" --min_total_DP "10" --keep_all_ref'
     max_amb_samples            = 10000000
     max_perc_amb_samples       = 10
-    publish_dir_mode           = 'symlink'
+    publish_dir_mode           = 'copy'
     rapidnj                    = true
     fasttree                   = true
     iqtree                     = false
@@ -198,7 +197,7 @@ manifest {
     description     = 'MycoSNP is a portable workflow for performing whole genome sequencing analysis of fungal organisms, including Candida auris. This method prepares the reference, performs quality control, and calls variants using a reference. MycoSNP generates several output files that are compatible with downstream analytic tools, such as those for used for phylogenetic tree-building and gene variant annotations.'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '1.0dev'
+    version         = 'v1.0'
 }
 
 // Load modules.config for DSL2 module specific options