Merge pull request #78 from CDCgov/bam_dev

version 3.1 bump

.github/workflows/test_pipeline.yaml

@@ -25,14 +25,16 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - name: Run Nextflow Illumina AQUASCOPE with Docker
         run: |
-          nextflow run main.nf --resume -profile docker,test_illumina -entry AQUASCOPE --outdir ~/testing/complete
+          nextflow run main.nf --resume -profile docker,test_illumina -entry AQUASCOPE --outdir ~/projects/complete
       - name: Set up Singularity
         uses: singularityhub/install-singularity@main
       - name: Run Nextflow Illumina QUALITY_ALIGN with Singularity
-        run: nextflow run main.nf --resume -profile singularity,test_illumina -entry QUALITY_ALIGN --outdir ~/testing/illumina
+        run: nextflow run main.nf --resume -profile singularity,test_illumina -entry QUALITY_ALIGN --outdir ~/projects/illumina/quality
       - name: Run Nextflow Illumina AQUASCOPE with Singularity
-        run: nextflow run main.nf --resume -profile singularity,test_illumina -entry AQUASCOPE --outdir ~/testing/complete
-      - name: Run Nextflow Illumina FREYJA_ONLY with Singularity
-        run: nextflow run main.nf --resume -profile singularity,test_bam -entry FREYJA_ONLY --outdir ~/testing/freyja
+        run: nextflow run main.nf --resume -profile singularity,test_illumina -entry AQUASCOPE --outdir ~/projects/illumina/complete
+      - name: Run Nextflow Illumina AQUASCOPE with Singularity
+        run: nextflow run main.nf --resume -profile singularity,test_bam -entry AQUASCOPE --outdir ~/projects/bam/complete
+      - name: Run Nextflow Ion Torrent FREYJA_ONLY with Singularity
+        run: nextflow run main.nf --resume -profile singularity,test_iontorrent -entry AQUASCOPE --outdir ~/projects/iontorrent/complete
       - name: Run Nextflow ONT AQUASCOPE with Singularity
-        run: nextflow run main.nf --resume -profile singularity,test_ont -entry AQUASCOPE --outdir ~/testing/ont
+        run: nextflow run main.nf --resume -profile singularity,test_ont -entry AQUASCOPE --outdir ~/projects/ont/complete

VERSION

@@ -1 +1 @@
-v3.0.0
+v3.1.0

assets/samplesheet_test_iontorrent.csv

@@ -1,2 +1,2 @@
 sample,platform,fastq_1,fastq_2,lr,bam_file,bedfile
-SAMPLE1,iontorrent,,,,test/sample1.bam,https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V3/nCoV-2019.primer.bed
+SAMPLE1,iontorrent,,,,test/Sample1.bam,https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V3/nCoV-2019.primer.bed

docs/user-guide/preparing-files.md

@@ -16,7 +16,9 @@ You will need to create a samplesheet with information about the samples you wou
     - [Ion-torrent example](https://github.com/CDCgov/aquascope/blob/main/assets/samplesheet_test_iontorrent.csv)	
 
 Notes:
+
 - Currently, Illumina, Ion-torrent and Oxford Nanopore platforms are supported in this pipeline.
+
 - Bedfiles can be a local file path or a raw.github url
 
 The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. It auto-detects sequencing platform (Illumina, Ion-torrent and Oxford nanopore) and determines which set of tools have to be run. The samplesheet must have 7 columns, and have to be in the same order as the header shown below.
@@ -32,7 +34,7 @@ SAMPLE1_SE,illumina,https://raw.githubusercontent.com/nf-core/test-datasets/vira
 | Column         | Description                                                                                                                                                                            | illumina | nanopore | iontorrent |
 |----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------|--------------|---------------------|
 | `sample`       | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | Required | Required | Required |
-| `platform`     | Sequencing platform. This entry will determine the type of sequencing used. It is an important entry as the decision to run a set of tools is determined by this entry.                | Required | Required | Required |
+| `platform`     | Sequencing platform. This entry will determine the type of sequencing used. It is an important entry as the decision to run a set of tools is determined by this entry. (Accepted entrys: "illumina", "nanopore", "iontorrent")                | Required | Required | Required |
 | `fastq_1`      | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             | Required | NA | NA |
 | `fastq_2`      | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                             | Required | NA | NA |
 | `lr`           | Full path to FastQ file for ONT long reads. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". fast5 files are not expected or accepted                            | NA | Required | NA |
@@ -42,6 +44,17 @@ SAMPLE1_SE,illumina,https://raw.githubusercontent.com/nf-core/test-datasets/vira
 
 ## Samplesheet for `FREYJA_ONLY` workflow
 
+Option 1. Create a samplesheet using the following reference: 
+
+    - [BAM example](../../assets/samplesheet_test_bam.csv)
+
+Option 2. Create samplesheet for primer trimmed bams using the python script `bin/bam_to_samplesheet.py`
+  ```
+  python bin/bam_to_samplesheet.py \
+    --directory <PATH_TO_BAM_FILES> \
+    --output <OUTPUT_FILE>"
+  ```
+
 ```console
 sample,bam_file
 Sample1,test/Sample1.bam
@@ -54,18 +67,7 @@ Sample2,test/Sample2.bam
 | `bam_file`     | Full path to BAM file for Ion-torrent short reads. File has to .bam strictly| 
 
 
-Option 1. Create a samplesheet using the following reference: 
-    - [BAM example](../../assets/samplesheet_test_bam.csv)
-
-Option 2. Create samplesheet for primer trimmed bams using the python script `bin/bam_to_samplesheet.py`
-  ```
-  python bin/bam_to_samplesheet.py \
-    --directory <PATH_TO_BAM_FILES> \
-    --output <OUTPUT_FILE>"
-  ```
-
 ## Prepare the config files
-Prepare the configuration files
 
 A. `scicomp.config`: CDC specific config to run on SciComp resources.
 

docs/user-guide/test-info.md

@@ -21,13 +21,13 @@ Test [samplesheet](https://github.com/CDCgov/aquascope/blob/dev/assets/sampleshe
 ### CDC Internal Users
 nextflow run \
 main.nf \
--profile test_illumina,singularity,scicomp_rosalind
+-profile test_illumina,singularity,scicomp_rosalind \
 -entry AQUASCOPE
 
 ### All Other Users
 nextflow run \
 main.nf \
--profile test_illumina,<docker,singularity,nf-core institutional config
+-profile test_illumina,<docker,singularity,nf-core institutional config> \
 -entry AQUASCOPE
 ```
 
@@ -38,13 +38,13 @@ Test [samplesheet](https://github.com/CDCgov/aquascope/blob/dev/assets/sampleshe
 ### CDC Internal Users
 nextflow run \
 main.nf \
--profile test_ont,singularity,scicomp_rosalind
+-profile test_ont,singularity,scicomp_rosalind \
 -entry AQUASCOPE
 
 ### All Other Users
 nextflow run \
 main.nf \
--profile test_ont,<docker,singularity,nf-core institutional config
+-profile test_ont,<docker,singularity,nf-core institutional config> \
 -entry AQUASCOPE
 ```
 
@@ -55,13 +55,13 @@ Test [samplesheet](https://github.com/CDCgov/aquascope/blob/main/assets/samplesh
 ### CDC Internal Users
 nextflow run \
 main.nf \
--profile test_bams,singularity,scicomp_rosalind
+-profile test_bams,singularity,scicomp_rosalind \
 -entry AQUASCOPE
 
 ### All Other Users
 nextflow run \
 main.nf \
--profile test_bams,<docker,singularity,nf-core institutional config
+-profile test_bams,<docker,singularity,nf-core institutional config> \
 -entry AQUASCOPE
 ```
 D. Test Iontorrent Input
@@ -71,13 +71,13 @@ Test [samplesheet](https://github.com/CDCgov/aquascope/blob/dev/assets/sampleshe
 ### CDC Internal Users
 nextflow run \
 main.nf \
--profile test_iontorrent,singularity,scicomp_rosalind
+-profile test_iontorrent,singularity,scicomp_rosalind \
 -entry AQUASCOPE
 
 ### All Other Users
 nextflow run \
 main.nf \
--profile test_iontorrent,<docker,singularity,nf-core institutional config
+-profile test_iontorrent,<docker,singularity,nf-core institutional config> \
 -entry AQUASCOPE
 ```