Merge pull request #131 from luslab/dev

v2.0 updates
nf-core · Jun 8, 2022 · f02083e · f02083e
2 parents dbaad8c + ca92a9b
commit f02083e
Show file tree

Hide file tree

Showing 17 changed files with 51 additions and 48 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -98,7 +98,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 | ---------- | ----------- | ----------- |
 | `samtools` | 1.14        | 1.15.1      |
 | `bowtie2`  | 2.4.2       | 2.4.4       |
-| `picard`   | 2.25.7      | 2.27.1      |
+| `picard`   | 2.25.7      | 2.27.2      |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 > **NB:** Dependency has been **added** if just the new version information is present.

diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -1,8 +1,5 @@
 #!/usr/bin/env python
 
-# This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv
-
-
 import os
 import sys
 import errno

diff --git a/conf/test.config b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-small.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv'
 
     // Genome references
     fasta              = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz'

diff --git a/conf/test_fasta_only.config b/conf/test_fasta_only.config
@@ -8,7 +8,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-small.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv'
 
     // Genome references
     fasta              = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz'

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     genome = 'GRCh38'
-    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all.csv'
 
     minimum_alignment_q_score = 10
 }
diff --git a/conf/test_full_multi.config b/conf/test_full_multi.config
@@ -15,7 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function with added fake replicates to test the full reporting functionality'
 
     genome = 'GRCh38'
-    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-multi-rep.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep.csv'
 
     minimum_alignment_q_score = 10
 }
diff --git a/conf/test_full_small.config b/conf/test_full_small.config
@@ -8,7 +8,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-small.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-small.csv'
 
     // Genome references
     fasta              = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz'

diff --git a/conf/test_full_small_local_zip.config b/conf/test_full_small_local_zip.config
@@ -8,7 +8,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-small.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-small.csv'
 
     // Genome references
     fasta              = '/home/runner/work/cutandrun/cutandrun/hg38-chr20.fa.gz'

diff --git a/conf/test_local_zip.config b/conf/test_local_zip.config
@@ -20,7 +20,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-small.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small.csv'
 
     // Genome references
     fasta              = '/home/runner/work/cutandrun/cutandrun/hg38-chr20.fa.gz'

diff --git a/conf/test_no_control.config b/conf/test_no_control.config
@@ -20,7 +20,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-noigg-small.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-noigg-small.csv'
 
     // Genome references
     fasta              = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz'

diff --git a/conf/test_tech_reps.config b/conf/test_tech_reps.config
@@ -20,7 +20,7 @@ params {
     max_time   = 6.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-small-tech-reps.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-small-tech-reps.csv'
 
     // Genome references
     fasta              = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz'

diff --git a/modules.json b/modules.json
@@ -46,7 +46,7 @@
                 "git_sha": "f0800157544a82ae222931764483331a81812012"
             },
             "picard/markduplicates": {
-                "git_sha": "20ebb89ff97a2665106be9cace5ccb9aa4eed1be"
+                "git_sha": "63db63757cab03cfa7a02c0d0f134b66fbfadea6"
             },
             "samtools/flagstat": {
                 "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
@@ -76,7 +76,7 @@
                 "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "untar": {
-                "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
+                "git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5"
             }
         }
     }

diff --git a/modules/nf-core/modules/picard/markduplicates/main.nf b/modules/nf-core/modules/picard/markduplicates/main.nf
diff --git a/modules/nf-core/modules/untar/main.nf b/modules/nf-core/modules/untar/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -252,7 +252,7 @@ manifest {
     description     = 'Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis.'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '1.1.0'
+    version = '2.0.0'
 }
 
 // Load flowswitch.config

diff --git a/tests/test_peak_callers.yml b/tests/test_peak_callers.yml
@@ -49,7 +49,7 @@
     - path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.macs2.peaks.bed_summits.bed
 
 - name: test_peak_callers_seacr_single_ctrl_multi_rep
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-multi-rep-single-ctrl.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep-single-ctrl.csv -c tests/config/nextflow.config
   tags:
     - test_peak_callers
     - test_peak_callers_ctrl_tests
@@ -60,7 +60,7 @@
     - path: results/03_peak_calling/04_called_peaks/h3k27me3_R2.seacr.peaks.bed.stringent.bed
 
 - name: test_peak_callers_seacr_multi_single_ctrl_multi_rep
-  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-multi-rep-multi-single-ctrl.csv -c tests/config/nextflow.config
+  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr --input https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet_2_0/test-GSE145187-all-multi-rep-multi-single-ctrl.csv -c tests/config/nextflow.config
   tags:
     - test_peak_callers
     - test_peak_callers_ctrl_tests