update

genemapis.sh

@@ -1,24 +1,24 @@
 #!/usr/bin/env sh
 
-#--- genemapgwas workflow wrapper ---#
+#--- genemapimputation workflow wrapper ---#
 
 function usage() {
    echo """
    ===================================================================
    GeneMAP-NGS ~ a wrapper for the nextflow-based genemapngs workflow
    ===================================================================
 
-   Usage: genemapngs <workflow> <profile> [options] ...
+   Usage: genemapis <workflow> <profile> [options] ...
 
            workflows:
            ---------
                test: Run test to see if workfow installed correctly.
               align: Check FASTQ or Alignment (BAM/CRAM) quality.
-               trim: Trim adapters and poor quality bases from reads.
-            varcall: Perform variant calling (both single and joint sample) in one run.
-           svarcall: Perform only sinlge sample variant calling to generate gVCF files.
-           jvarcall: Perform only joint (multi-sample) variant calling with pre-existing gVCF files.
-          varfilter: Filter variant calls in VCF/BCF files.
+               xxxx: Trim adapters and poor quality bases from reads.
+            xxxxxxx: .
+           xxxxxxxx: .
+           xxxxxxxx: .
+          xxxxxxxxx: .
 
 
            profiles: <executor>,<container>,<reference>
@@ -30,8 +30,8 @@ function usage() {
 
            examples:
            ---------
-         genemapngs qc slurm,singularity,hg38 [options]
-         genemapngs align local,singularity,hg19 --bfile BEDFILE --out MYOUT --outdir MYPATH --pheno_file MYPHENO
+         genemapngs test slurm,singularity,hg38 [options]
+         genemapngs align local,singularity,hg19 --vcf my-vcf.vcf.gz 
    """
 }
 

modules/phasing_and_imputation.nf

@@ -213,7 +213,12 @@ process checkStrand() {
     label 'beagle'
     label 'alignGenotypes'
     publishDir \
-        path: "${params.output_dir}/aligned/", \
+        pattern: "chr${chrom}-aligned.vcf.gz", \
+        path: "${params.output_dir}/aligned/vcf/", \
+        mode: 'copy'
+    publishDir \
+        pattern: "chr${chrom}-aligned.log", \
+        path: "${params.output_dir}/aligned/logs/", \
         mode: 'copy'
     input:
 	tuple \

system.config

@@ -1,8 +1,18 @@
+params { // one-time system configuration //
+
+  account = 'NULL'
+  queue = 'NULL'
+  containers_dir = 'NULL'
+  email = 'NULL'
+  study_title = 'NULL'
+
+  /************************************************************************************************
+  ~ account: If using SLURM or PBSPRO, provide your cluster project or account name.
+  ~ queue: If using SLURM or PBSPRO, specify the queue or partition name.
+  ~ containers_dir: If using singularity containers, provide a path where the images will be stored.
+    NB: The path should have sufficient storage capacity.
+  ~ email: If you wish to receive information on job status.
+  ~ study_title: The name of your study/project.
+  /***********************************************************************************************/
 
-params { // one time system configuration
-   account		= "humgen" 			// if using SLURM or PBSPRO, provide your cluster project or account name
-   queue		= "sadacc-long" 		// if using SLURM or PBSPRO, specify the queue or partition name
-   njobs		= 10 				// number of jobs to submit at once each time
-   containers_dir	= "/scratch/eshkev001/containers/" // if using singularity containers, provide a path where the images will be stored. NB: The path should have sufficient storage capacity
-   email		= 'NULL'
 }