move blacklists, update nextflow.config, add test dataset

PC.nf

@@ -8,7 +8,6 @@ nextflow.enable.dsl=2
 // import modules
 include { INPUT_CHECK } from './modules/local/input_check.nf'
 include { generate_whitelist as whitelist_experimental ; generate_whitelist as whitelist_spikein } from './modules/local/generate_whitelist.nf'
-include { CUSTOM_GETCHROMSIZES } from './modules/nf-core/modules/custom/getchromsizes/main.nf'
 include { FASTQC_TRIMGALORE } from './modules/local/fastqc_trimgalore.nf'
 include { BOWTIE2_BUILD as BOWTIE2_BUILD_EXPERIMENTAL ; BOWTIE2_BUILD as BOWTIE2_BUILD_SPIKEIN } from './modules/nf-core/modules/bowtie2/build/main.nf'
 include { CHROMAP_INDEX as CHROMAP_INDEX_EXPERIMENTAL ; CHROMAP_INDEX as CHROMAP_INDEX_SPIKEIN } from './modules/nf-core/modules/chromap/index/main.nf'
@@ -43,13 +42,19 @@ workflow {
         params.skip_trimming
     )
 
-    // Setting up channels based on parameter selections for experimental and spike-in genomes. Create index for chosen aligner if not supplied. 
+    // Setting up channels based on parameter selections for experimental and spike-in genomes.
     ch_experimental_fa = Channel.empty()
     ch_spikein_fa = Channel.empty()
     ch_experimental_bowtie2_index = Channel.empty()
     ch_experimental_chro_index = Channel.empty()
     ch_spikein_bowtie2_index = Channel.empty()
     ch_spikein_chro_index = Channel.empty()
+    ch_experimental_gtf = Channel.empty()
+    ch_experimental_blacklist = Channel.empty()
+    ch_spikein_blacklist = Channel.empty()
+    ch_macs_gsize = Channel.empty()
+
+    // Create index for chosen aligner if not supplied and set up channels for experimental and spike-in genomes
     if (params.experimental == 'human') {
         ch_experimental_fa = params.human_fa
         if (params.aligner == 'chromap') {
@@ -268,10 +273,6 @@ workflow {
         ch_spikein_blacklist = params.fly_blacklist
     }
 
-    CUSTOM_GETCHROMSIZES (
-        ch_experimental_fa
-    )
-
     whitelist_experimental (
         ch_experimental_fa,
         ch_experimental_blacklist
@@ -619,7 +620,7 @@ workflow {
 
     macs2_bdgcmp (
         macs2_peakcalling.out.chip_ctrl_bdg,
-        CUSTOM_GETCHROMSIZES.out.sizes,
+        whitelist_experimental.out.sizes,
         params.macs2_bigwig_method
     )
 

Run_example.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+#SBATCH --cpus-per-task=1
+#SBATCH --job-name=RunPerCell
+
+nextflow run PC.nf \
+    -profile singularity \
+    --human_fa '/path/to/downloaded/genome.fa' \
+    --mouse_fa '/path/to/downloaded/genome.fa'

assets/dm6-blacklist.v2.bed.gz

@@ -0,0 +1 @@
+{"payload":{"allShortcutsEnabled":false,"fileTree":{"lists":{"items":[{"name":"Blacklist_v1","path":"lists/Blacklist_v1","contentType":"directory"},{"name":"metadata","path":"lists/metadata","contentType":"directory"},{"name":"ce10-blacklist.v2.bed.gz","path":"lists/ce10-blacklist.v2.bed.gz","contentType":"file"},{"name":"ce11-blacklist.v2.bed.gz","path":"lists/ce11-blacklist.v2.bed.gz","contentType":"file"},{"name":"dm3-blacklist.v2.bed.gz","path":"lists/dm3-blacklist.v2.bed.gz","contentType":"file"},{"name":"dm6-blacklist.v2.bed.gz","path":"lists/dm6-blacklist.v2.bed.gz","contentType":"file"},{"name":"hg19-blacklist-README.pdf","path":"lists/hg19-blacklist-README.pdf","contentType":"file"},{"name":"hg19-blacklist.v2.bed.gz","path":"lists/hg19-blacklist.v2.bed.gz","contentType":"file"},{"name":"hg38-blacklist.v2.bed.gz","path":"lists/hg38-blacklist.v2.bed.gz","contentType":"file"},{"name":"mm10-blacklist.v2.bed.gz","path":"lists/mm10-blacklist.v2.bed.gz","contentType":"file"}],"totalCount":10},"":{"items":[{"name":"bamtools","path":"bamtools","contentType":"submodule","submoduleUrl":"/pezmaster31/bamtools/tree/cbca090607f2154aa19c20ca778c3d067384b606","submoduleDisplayName":"bamtools 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example/example_input.csv

@@ -0,0 +1,5 @@
+sample,fastq_1,fastq_2,antibody,control
+MYOD_1,./example/read5.fq.gz,./example/read6.fq.gz,MYOD,Input_1
+MYOD_2,./example/read7.fq.gz,./example/read8.fq.gz,MYOD,Input_2
+Input_1,./example/read1.fq.gz,./example/read2.fq.gz,,
+Input_2,./example/read3.fq.gz,./example/read4.fq.gz,,

nextflow.config

@@ -27,8 +27,8 @@ params {
     max_time = 120.h  
 
     // input/output default params
-    input = '/home/gdstantonlab/lab/Lex/pipeline/test_input_reps.csv'
-    outdir = './PerCell_Output/'
+    input = 'example/example_input.csv'
+    outdir = 'PerCell_Output'
     aligner = 'bowtie2'
     experimental = 'human'
     spikein = 'mouse'
@@ -41,10 +41,10 @@ params {
     mouse_fa = ''
     zebrafish_fa = ''
     fly_fa = ''
-    human_blacklist = './bin/hg38-blacklist.v2.bed.gz'
-    mouse_blacklist = './bin/mm10-blacklist.v2.Liftover.mm39.bed.gz'
-    zebrafish_blacklist = './bin/blank_blacklist.bed.gz'
-    fly_blacklist = './bin//dm6-blacklist.v2.bed.gz'
+    human_blacklist = "$projectDir/assets/hg38-blacklist.v2.bed.gz"
+    mouse_blacklist = "$projectDir/assets/mm10-blacklist.v2.Liftover.mm39.bed.gz"
+    zebrafish_blacklist = "$projectDir/assets/blank_blacklist.bed.gz"
+    fly_blacklist = "$projectDir/assets/dm6-blacklist.v2.bed.gz"
 
     // params for trimgalore
     clip_r1 = 0
@@ -96,7 +96,6 @@ params {
     skip_idr = true
     idr_cutoff = 0.05
     skip_consensus = true
-
 }
 
 // Load modules.config for DSL2 module specific options