Merge branch '36-astrocyte-documentation' into 'master'

Resolve "Update Astrocyte documentation and errors"

Closes #36

See merge request !30

.gitlab-ci.yml

@@ -32,7 +32,7 @@ single_end_mouse:
   only:
     - master
   script:
-  - nextflow run workflow/main.nf --astrocyte 'true' -resume
+  - nextflow run workflow/main.nf --astrocyte true -resume
   - pytest -m singleend
   artifacts:
     expire_in: 2 days
@@ -44,7 +44,7 @@ paired_end_human:
   except:
     - master
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte 'false' -resume
+  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume
   - pytest -m pairedend
   artifacts:
     expire_in: 2 days
@@ -56,7 +56,7 @@ single_end_diff:
   except:
     - master
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte 'false' -resume
+  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false -resume
   - pytest -m singlediff
   artifacts:
     expire_in: 2 days
@@ -66,7 +66,7 @@ paired_end_diff:
     - master
   stage: multiple
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte 'false' -resume
+  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume
   - pytest -m paireddiff
   artifacts:
     expire_in: 2 days
@@ -76,7 +76,7 @@ single_end_skip:
   only:
     - master
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --astrocyte 'false' -resume
+  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --astrocyte false -resume
   - pytest -m singleskip_true
   artifacts:
     expire_in: 2 days

README.md

@@ -5,6 +5,7 @@
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.24.0-brightgreen.svg
 )](https://www.nextflow.io/)
 [![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.1.0-blue.svg)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2648845.svg)](https://doi.org/10.5281/zenodo.2648845)
 
 
 ## Introduction

astrocyte_pkg.yml

@@ -101,8 +101,8 @@ workflow_parameters:
     type: select
     required: true
     choices:
-      - [ 'true', 'True']
-      - [ 'false', 'False']
+      - [ 'true', 'true']
+      - [ 'false', 'false']
     description: |
       In single-end sequencing, the sequencer reads a fragment from only one
       end to the other, generating the sequence of base pairs. In paired-end
@@ -128,6 +128,24 @@ workflow_parameters:
     description: |
       Reference species and genome used for alignment and subsequent analysis.
 
+  - id: skipDiff
+    type: select
+    required: true
+    choices:
+      - [ 'true', 'true']
+      - [ 'false', 'false']
+    description: |
+      Run differential peak analysis
+
+  - id: skipMotif
+    type: select
+    required: true
+    choices:
+      - [ 'true', 'true']
+      - [ 'false', 'false']
+    description: |
+      Run motif calling
+
   - id: astrocyte
     type: select
     choices:

docs/design_example.csv

-SampleID,Tissue,Factor,Condition,Replicate,Peaks,bamReads,bamControl,ControlID,PeakCaller
-A_1,A,H3K27AC,A,1,A_1.broadPeak,A_1.bam,A_1_input.bam,A_1_input,bed
-A_2,A,H3K27AC,A,2,A_2.broadPeak,A_2.bam,A_2_input.bam,A_2_input,bed
-B_1,B,H3K27AC,B,1,B_1.broadPeak,B_1.bam,B_1_input.bam,B_1_input,bed
-B_2,B,H3K27AC,B,2,B_2.broadPeak,B_2.bam,B_2_input.bam,B_2_input,bed
-C_1,C,H3K27AC,C,1,C_1.broadPeak,C_1.bam,C_1_input.bam,C_1_input,bed
-C_2,C,H3K27AC,C,2,C_2.broadPeak,C_2.bam,C_2_input.bam,C_2_input,bed

docs/design_example.txt

+sample_id	experiment_id	biosample	factor	treatment	replicate	control_id	fastq_read1
+A1	A	tissueA	H3K27AC	None	1	B1	A1.fastq.gz
+A2	A	tissueA	H3K27AC	None	2	B2	A2.fastq.gz
+B1	B	tissueB	Input	None	1	B1	B1.fastq.gz
+B2	A	tissueB	Input	None	2	B2	B2.fastq.gz

docs/index.md

-# Astrocyte ChIPseq analysis Workflow Package
+# BICF ChIP-seq Analysis Workflow
 
 ## Introduction
 **ChIP-seq Analysis** is a bioinformatics best-practice analysis pipeline used for chromatin immunoprecipitation (ChIP-seq) data analysis.
@@ -7,16 +7,16 @@ The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow
 
 ### Pipeline Steps
 
-1) Trim adaptors TrimGalore!
-2) Align with BWA
-3) Filter reads with Sambamba  S
-4) Quality control with DeepTools
-5) Calculate Cross-correlation using SPP and PhantomPeakQualTools
-6) Signal profiling using MACS2
-7) Call consenus peaks
-8) Annotate all peaks using ChipSeeker
-9) Use MEME-ChIP to find motifs in original peaks
-10) Find differential expressed peaks using DiffBind (If more than 1 experiment)
+  1) Trim adaptors TrimGalore!
+  2) Align with BWA
+  3) Filter reads with Sambamba  S
+  4) Quality control with DeepTools
+  5) Calculate Cross-correlation using SPP and PhantomPeakQualTools
+  6) Signal profiling using MACS2
+  7) Call consenus peaks
+  8) Annotate all peaks using ChipSeeker
+  9) Use MEME-ChIP to find motifs in original peaks
+  10) Find differential expressed peaks using DiffBind (If more than 1 experiment)
 
 
 ## Workflow Parameters
@@ -25,41 +25,35 @@ The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow
     pairedEnd - Choose True/False if data is paired-end
     design - Choose the file with the experiment design information. TSV format
     genome - Choose a genomic reference (genome).
+    skipDiff - Choose True/False if data if you want to run Differential Peaks
+    skipMotif - Choose True/False if data if you want to run Motif Calling
 
 
 ## Design file
 
- The following columns are necessary, must be named as in template. An design file template can be downloaded [HERE](https://git.biohpc.swmed.edu/bchen4/chipseq_analysis/raw/master/docs/design_example.csv)
-
-    SampleID
-        The id of the sample. This will be the header in output files, please make sure it is concise
-    Tissue
-        Tissue of the sample
-    Factor
-        Factor of the experiment
-    Condition
-	    This is the group that will be used for pairwise differential expression analysis
-	Replicate
-	    Replicate id
-    Peaks
-        The file name of the peak file for this sample
-    bamReads
-        The file name of the IP BAM for this sample
-    bamControl
-        The file name of the control BAM for this sample
-    ContorlID
-        The id of the control sample
-    PeakCaller
-        The peak caller used
-
+ The following columns are necessary, must be named as in template. An design file template can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/docs/design_example.txt)
+
+    sample_id
+        The id of the sample. This will be the name used in output files, please make sure it is concise and informative.
+    experiment_id
+        The id of the experiment. Used for grouping replicates.
+    biosample
+        The name of the biological sample.
+    factor
+        Factor of the experiment.
+    treatment
+        Treatment used in experiment.
+    replicate
+        Replicate number.
+    control_id
+	    The sample_id of the control used for this sample.
+    fastq_read1
+      File name of fastq file, if paired-end this is read1.
+    fastq_read2
+      File name of read2 (for paired-end), not needed for single-end data.
 
 
 ### Credits
-This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility (BICF), Department of Bioinformatics
-
-### References
+This worklow is was developed jointly with the [Bioinformatic Core Facility (BICF), Department of Bioinformatics](http://www.utsouthwestern.edu/labs/bioinformatics/)
 
-* ChipSeeker: http://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
-* DiffBind: http://bioconductor.org/packages/release/bioc/html/DiffBind.html
-* Deeptools: https://deeptools.github.io/
-* MEME-ChIP: http://meme-suite.org/doc/meme-chip.html
+Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**.

docs/references.md

@@ -50,3 +50,8 @@
 
 16. **MultiQc**:
   * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354 ](https://dx.doi.org/10.1093/bioinformatics/btw354)
+
+17. **BICF ChIP-seq Analysis Workflow**:
+  * Venkat S. Malladi and Beibei Chen. (2019). BICF ChIP-seq Analysis Workflow (publish_1.0.0). Zenodo. doi:[10.5281/zenodo.2648845](https://doi.org/10.5281/zenodo.2648845)
+
+Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**.

workflow/main.nf

@@ -5,14 +5,14 @@
 
 // Define Input variables
 params.reads = "$baseDir/../test_data/*.fastq.gz"
-params.pairedEnd = 'false'
+params.pairedEnd = false
 params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt"
 params.genome = 'GRCm38'
 params.cutoffRatio = 1.2
 params.outDir= "$baseDir/output"
 params.extendReadsLen = 100
 params.topPeakCount = 600
-params.astrocyte = 'false'
+params.astrocyte = false
 params.skipDiff = false
 params.skipMotif = false
 params.references = "$baseDir/../docs/references.md"
@@ -56,6 +56,7 @@ readsList = Channel
   .collectFile( name: 'fileList.tsv', newLine: true )
 
 // Define regular variables
+pairedEnd = params.pairedEnd
 designFile = params.designFile
 genomeSize = params.genomeSize
 genome = params.genome
@@ -70,12 +71,6 @@ skipMotif = params.skipMotif
 references = params.references
 multiqc = params.multiqc
 
-if (params.pairedEnd == 'false'){
-  pairedEnd = false
-} else {
-  pairedEnd = true
-}
-
 // Check design file for errors
 process checkDesignFile {