Merge pull request #80 from drpatelh/master

Update docs and images

Author: drpatelh

README.md

@@ -55,9 +55,7 @@ The nf-core/chipseq pipeline comes with documentation about the pipeline, found
 5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
 
 ## Credits
-These scripts were written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/)
-at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden.
-Originally written by Chuan Wang ([@chuan-wang](https://github.com/chuan-wang)) and Phil Ewels ([@ewels](https://github.com/ewels)), and re-implemented by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) at [The Francis Crick Institute](https://www.crick.ac.uk/), London.
+These scripts were orginally written by Chuan Wang ([@chuan-wang](https://github.com/chuan-wang)) and Phil Ewels ([@ewels](https://github.com/ewels)) for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. It has since been re-implemented by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) at [The Francis Crick Institute](https://www.crick.ac.uk/), London.
 
 ## Citation
 

assets/design_pe.csv

@@ -1,8 +1,21 @@
-group,replicate,fastq_1,fastq_2,control
-control,1,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,
-control,2,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A2_S2_L002_R2_001.fastq.gz,
-control,3,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A3_S3_L002_R2_001.fastq.gz,
-treatment,1,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,/path/to/fastq/files/AEG588A4_S4_L003_R2_001.fastq.gz,
-treatment,2,/path/to/fastq/files/AEG588A5_S5_L003_R1_001.fastq.gz,/path/to/fastq/files/AEG588A5_S5_L003_R2_001.fastq.gz,
-treatment,3,/path/to/fastq/files/AEG588A6_S6_L003_R1_001.fastq.gz,/path/to/fastq/files/AEG588A6_S6_L003_R2_001.fastq.gz,
-treatment,3,/path/to/fastq/files/AEG588A6_S6_L004_R1_001.fastq.gz,/path/to/fastq/files/AEG588A6_S6_L004_R2_001.fastq.gz,
+group,replicate,fastq_1,fastq_2,antibody,control
+WT_BCATENIN_IP,1,BLA203A1_S27_L006_R1_001.fastq.gz,BLA203A1_S27_L006_R2_001.fastq.gz,BCATENIN,WT_INPUT
+WT_BCATENIN_IP,2,BLA203A25_S16_L001_R1_001.fastq.gz,BLA203A25_S16_L001_R2_001.fastq.gz,BCATENIN,WT_INPUT
+WT_BCATENIN_IP,2,BLA203A25_S16_L002_R1_001.fastq.gz,BLA203A25_S16_L002_R2_001.fastq.gz,BCATENIN,WT_INPUT
+WT_BCATENIN_IP,3,BLA203A49_S40_L001_R1_001.fastq.gz,BLA203A49_S40_L001_R2_001.fastq.gz,BCATENIN,WT_INPUT
+NAIVE_BCATENIN_IP,1,BLA203A7_S60_L001_R1_001.fastq.gz,BLA203A7_S60_L001_R2_001.fastq.gz,BCATENIN,NAIVE_INPUT
+NAIVE_BCATENIN_IP,2,BLA203A43_S34_L001_R1_001.fastq.gz,BLA203A43_S34_L001_R2_001.fastq.gz,BCATENIN,NAIVE_INPUT
+NAIVE_BCATENIN_IP,2,BLA203A43_S34_L002_R1_001.fastq.gz,BLA203A43_S34_L002_R2_001.fastq.gz,BCATENIN,NAIVE_INPUT
+NAIVE_BCATENIN_IP,3,BLA203A64_S55_L001_R1_001.fastq.gz,BLA203A64_S55_L001_R2_001.fastq.gz,BCATENIN,NAIVE_INPUT
+WT_TCF4_IP,1,BLA203A3_S29_L006_R1_001.fastq.gz,BLA203A3_S29_L006_R2_001.fastq.gz,TCF4,WT_INPUT
+WT_TCF4_IP,2,BLA203A27_S18_L001_R1_001.fastq.gz,BLA203A27_S18_L001_R2_001.fastq.gz,TCF4,WT_INPUT
+WT_TCF4_IP,3,BLA203A51_S42_L001_R1_001.fastq.gz,BLA203A51_S42_L001_R2_001.fastq.gz,TCF4,WT_INPUT
+NAIVE_TCF4_IP,1,BLA203A9_S62_L001_R1_001.fastq.gz,BLA203A9_S62_L001_R2_001.fastq.gz,TCF4,NAIVE_INPUT
+NAIVE_TCF4_IP,2,BLA203A45_S36_L001_R1_001.fastq.gz,BLA203A45_S36_L001_R2_001.fastq.gz,TCF4,NAIVE_INPUT
+NAIVE_TCF4_IP,3,BLA203A66_S57_L001_R1_001.fastq.gz,BLA203A66_S57_L001_R2_001.fastq.gz,TCF4,NAIVE_INPUT
+WT_INPUT,1,BLA203A6_S32_L006_R1_001.fastq.gz,BLA203A6_S32_L006_R2_001.fastq.gz,,
+WT_INPUT,2,BLA203A30_S21_L001_R1_001.fastq.gz,BLA203A30_S21_L001_R2_001.fastq.gz,,
+WT_INPUT,3,BLA203A31_S21_L003_R1_001.fastq.gz,BLA203A31_S21_L003_R2_001.fastq.gz,,
+NAIVE_INPUT,1,BLA203A12_S3_L001_R1_001.fastq.gz,BLA203A12_S3_L001_R2_001.fastq.gz,,
+NAIVE_INPUT,2,BLA203A48_S39_L001_R1_001.fastq.gz,BLA203A48_S39_L001_R2_001.fastq.gz,,
+NAIVE_INPUT,3,BLA203A49_S1_L006_R1_001.fastq.gz,BLA203A49_S1_L006_R2_001.fastq.gz,,

assets/design_se.csv

@@ -1,8 +1,21 @@
-group,replicate,fastq_1,fastq_2,control
-control,1,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,,
-control,2,/path/to/fastq/files/AEG588A2_S2_L002_R1_001.fastq.gz,,
-control,3,/path/to/fastq/files/AEG588A3_S3_L002_R1_001.fastq.gz,,
-treatment,1,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,
-treatment,2,/path/to/fastq/files/AEG588A5_S5_L003_R1_001.fastq.gz,,
-treatment,3,/path/to/fastq/files/AEG588A6_S6_L003_R1_001.fastq.gz,,
-treatment,3,/path/to/fastq/files/AEG588A6_S6_L004_R1_001.fastq.gz,,
+group,replicate,fastq_1,fastq_2,antibody,control
+WT_BCATENIN_IP,1,BLA203A1_S27_L006_R1_001.fastq.gz,,BCATENIN,WT_INPUT
+WT_BCATENIN_IP,2,BLA203A25_S16_L001_R1_001.fastq.gz,,BCATENIN,WT_INPUT
+WT_BCATENIN_IP,2,BLA203A25_S16_L002_R1_001.fastq.gz,,BCATENIN,WT_INPUT
+WT_BCATENIN_IP,3,BLA203A49_S40_L001_R1_001.fastq.gz,,BCATENIN,WT_INPUT
+NAIVE_BCATENIN_IP,1,BLA203A7_S60_L001_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT
+NAIVE_BCATENIN_IP,2,BLA203A43_S34_L001_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT
+NAIVE_BCATENIN_IP,2,BLA203A43_S34_L002_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT
+NAIVE_BCATENIN_IP,3,BLA203A64_S55_L001_R1_001.fastq.gz,,BCATENIN,NAIVE_INPUT
+WT_TCF4_IP,1,BLA203A3_S29_L006_R1_001.fastq.gz,,TCF4,WT_INPUT
+WT_TCF4_IP,2,BLA203A27_S18_L001_R1_001.fastq.gz,,TCF4,WT_INPUT
+WT_TCF4_IP,3,BLA203A51_S42_L001_R1_001.fastq.gz,,TCF4,WT_INPUT
+NAIVE_TCF4_IP,1,BLA203A9_S62_L001_R1_001.fastq.gz,,TCF4,NAIVE_INPUT
+NAIVE_TCF4_IP,2,BLA203A45_S36_L001_R1_001.fastq.gz,,TCF4,NAIVE_INPUT
+NAIVE_TCF4_IP,3,BLA203A66_S57_L001_R1_001.fastq.gz,,TCF4,NAIVE_INPUT
+WT_INPUT,1,BLA203A6_S32_L006_R1_001.fastq.gz,,,
+WT_INPUT,2,BLA203A30_S21_L001_R1_001.fastq.gz,,,
+WT_INPUT,3,BLA203A31_S21_L003_R1_001.fastq.gz,,,
+NAIVE_INPUT,1,BLA203A12_S3_L001_R1_001.fastq.gz,,,
+NAIVE_INPUT,2,BLA203A48_S39_L001_R1_001.fastq.gz,,,
+NAIVE_INPUT,3,BLA203A49_S1_L006_R1_001.fastq.gz,,,

conf/test.config

@@ -16,7 +16,7 @@ params {
   max_time = 12.h
 
   // Input data
-  design = 'https://raw.githubusercontent.com/drpatelh/chipseq/master/design.csv'
+  design = 'https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/design.csv'
 
   // Genome references
   fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa'
@@ -26,5 +26,5 @@ params {
   macs_gsize = 1.2e7
 
   // For speed to avoid CI time-out
-  fingerprintBins = 100
+  fingerprint_bins = 100
 }