Hotfix for error related to --bcs_db_rootdir

LICENSE.md

@@ -41,7 +41,7 @@ SOFTWARE.
 \
  
 
-Major portions of **CPIPES** are built on modified versions of many modules, scripts and libraries from [nf-core/modules](https://github.com/nf-core/modules) and [nf-core/rnaseq](https://github.com/nf-core/rna-seq) which are originally licensed under:
+Major portions of **CPIPES** are built on modified versions of many modules, scripts and libraries from [nf-core/modules](https://github.com/nf-core/modules) and [nf-core/rnaseq](https://github.com/nf-core/rnaseq) which are originally licensed under:
 
 ```text
 MIT License

README.md

@@ -59,8 +59,8 @@ This work is currently unpublished. If you are making use of this analysis pipel
 
 ---
 
-1. [Nextflow version 22.10.0](https://github.com/nextflow-io/nextflow/releases/download/v22.10.0/nextflow-22.10.0-all).
-    - Make sure to rename the downloaded binary to `nextflow` and also make sure that it is made available in your `$PATH`.
+1. [Nextflow version 22.10.0](https://github.com/nextflow-io/nextflow/releases/download/v22.10.0/nextflow).
+    - Make the `nextflow` binary executable (`chmod 755 nextflow`) and also make sure that it is made available in your `$PATH`.
     - If your existing `JAVA` install does not support the newest **Nextflow** version, you can try **Amazon**'s `JAVA` (OpenJDK):  [Corretto](https://corretto.aws/downloads/latest/amazon-corretto-17-x64-linux-jdk.tar.gz).
 2. Either of `micromamba` or `docker` or `singularity` installed and made available in your `$PATH`.
     - Running the workflow via `micromamba` software provisioning is **preferred** as it does not require any `sudo` or `admin` privileges or any other configurations with respect to the various container providers.

conf/multiqc/bettercallsal_mqc.yml

@@ -2,7 +2,7 @@ title: CPIPES Report
 intro_text: >
     CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, FDA based on NEXTFLOW DSL2. 
 report_comment: >
-    This report has been generated by the <a href="https://github.com/CFSAN-Biostatistics/bettercallsal/readme/Workflow_Name_Placeholder.md" target="_blank">CPIPES - Workflow_Name_Placeholder</a>
+    This report has been generated by the <a href="https://github.com/CFSAN-Biostatistics/bettercallsal/blob/master/readme/Workflow_Name_Placeholder.md" target="_blank">CPIPES - Workflow_Name_Placeholder</a>
     analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory.
 report_header_info:
     - CPIPES Version: CPIPES_Version_Placeholder

lib/help/tuspy.nf

@@ -20,7 +20,7 @@ def tuspyHelp(params) {
                 'field separator, | and ' +
                 '5 fields: serotype|asm_lvl|asm_url|snp_cluster_id' +
                 'Ex: serotype=Derby,antigen_formula=4:f,g:-|Scaffold|402440|ftp://...' +
-                '|PDS000096654.2. Mentioning this option will create a pickle file for the' +
+                '|PDS000096654.2. Mentioning this option will create a pickle file for the ' +
                 'provided metadata and exits.' +
                 " Default: ${params.tuspy_s}",
             cliflag: '-s',

readme/bettercallsal.md

@@ -104,7 +104,7 @@ Workflow                        : bettercallsal
 
 Author                          : Kranti Konganti
 
-Version                         : 0.2.0
+Version                         : 0.2.1
 
 
 Usage                           : cpipes --pipeline bettercallsal [options]
@@ -291,7 +291,7 @@ Other options                   :
                                   serotype=Derby,antigen_formula=4:f,g:-|
                                   Scaffold|402440|ftp://...|PDS000096654.2.
                                   Mentioning this option will create a pickle
-                                  file for theprovided metadata and exits.
+                                  file for the provided metadata and exits.
                                   Default: false
 
 --tuspy_m                       : Absolute UNIX path to mash screen results
@@ -377,7 +377,7 @@ Other options                   :
 
 --kmaalign_bcg                  : Maintain insignificant gaps. Default: false
 
---kmaalign_ID                   : Minimum consensus ID. Default: 5.0
+--kmaalign_ID                   : Minimum consensus ID. Default: 10.0
 
 --kmaalign_md                   : Minimum depth. Default: false
 

readme/bettercallsal_db.md

@@ -69,7 +69,7 @@ Workflow                        : bettercallsal_db
 
 Author                          : Kranti Konganti
 
-Version                         : 0.2.0
+Version                         : 0.2.1
 
 
 Required                        :

workflows/bettercallsal.nf

@@ -164,7 +164,7 @@ workflow BETTERCALLSAL {
             .collect()
             .set { ch_salmon_res_dirs }
 
-        BCS_RESULTS( ch_salmon_res_dirs )
+        BCS_RESULTS ( ch_salmon_res_dirs )
 
         DUMP_SOFTWARE_VERSIONS (
             software_versions

workflows/bettercallsal_db.nf

@@ -31,7 +31,7 @@ include { DUMP_SOFTWARE_VERSIONS   } from "${params.modules}${params.fs}custom${
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    INPUTS AND ANY CHECKS FOR THE BETTERCALLSAL WORKFLOW
+    INPUTS AND ANY CHECKS FOR THE BETTERCALLSAL_DB WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
@@ -43,7 +43,7 @@ if (!params.output) {
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN THE BETTERCALLSAL WORKFLOW
+    RUN THE BETTERCALLSAL_DB WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
@@ -153,7 +153,7 @@ workflow.onError {
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    HELP TEXT METHODS FOR BETTERCALLSAL WORKFLOW
+    HELP TEXT METHODS FOR BETTERCALLSAL_DB WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 

workflows/conf/bettercallsal.config

@@ -1,8 +1,8 @@
 params {
     workflow_conceived_by = 'Kranti Konganti'
     workflow_built_by = 'Kranti Konganti'
-    workflow_version = '0.2.0'
-    bcs_root_dbdir = '/hpc/db/bettercallsal/latest'
+    workflow_version = '0.2.1'
+    bcs_root_dbdir = '/tmp'
     bcs_db_mode = 'snp'
     bcs_db_mode_index = (params.bcs_db_mode ==~ /snp/ ? '_cluster' : '_serotype')
     bbmerge_run = true

workflows/conf/bettercallsal_db.config

@@ -1,7 +1,7 @@
 params {
     workflow_conceived_by = 'Kranti Konganti'
     workflow_built_by = 'Kranti Konganti'
-    workflow_version = '0.2.0'
+    workflow_version = '0.2.1'
     pdg_release = 'PDG000000002.2507'
     ncbi_asm_suffix = '_genomic.fna.gz'
     wcomp_serocol = false