Merge pull request #963 from lldelisle/update_chip_pe

Update ChIP PE

Author: mvdbeek

workflows/epigenetics/chipseq-pe/CHANGELOG.md

@@ -1,5 +1,14 @@
 # Changelog
 
+## [1.0] - 2025-10-03
+
+### Tool change
+
+- The workflow now uses fastp instead of cutadapt.
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0`
+
 ## [0.15] - 2025-06-09
 
 ### Automatic update

workflows/epigenetics/chipseq-pe/README.md

@@ -6,14 +6,14 @@
 
 ## Inputs values
 
-- adapters sequences: this depends on the library preparation. If you don't know, use FastQC to determine if it is Truseq or Nextera.
-- reference_genome: this field will be adapted to the genomes available for bowtie2.
-- effective_genome_size: this is used by MACS2 and may be entered manually (indications are provided for heavily used genomes).
-- normalize_profile: Whether you want to have a profile normalized as Signal to Million Fragments.
+- Percentage of bad quality bases per read: fastp will discard any read which has more than this percentage of bases with a quality below 30. This depends on your read length.
+- Reference genome: this field will be adapted to the genomes available for bowtie2.
+- Effective genome size: this is used by MACS2 and may be entered manually (indications are provided for heavily used genomes).
+- Normalize profile: Whether you want to have a profile normalized as Signal to Million Fragments.
 
 ## Processing
 
-- The workflow will remove illumina adapters and low quality bases and filter out any pair with mate smaller than 15bp.
+- The workflow will remove illumina adapters using read overlap and filter out any read smaller than 15bp after adapter removal. All reads with too many low quality bases will be discarded.
 - The filtered reads are mapped with bowtie2 with default parameters.
 - The BAM is filtered to keep only MAPQ30 and concordant pairs.
 - The peaks are called with MACS2 which at the same time generates a coverage file (normalized or not).

workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml

@@ -16,79 +16,78 @@
           class: File
           location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read2.fastq.gz
           filetype: fastqsanger.gz
-    adapter_forward: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
-    adapter_reverse: 'GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'
-    reference_genome: 'mm10'
-    effective_genome_size: 1870000000
-    normalize_profile: true
+    Percentage of bad quality bases per read: 70
+    Reference genome: 'mm10'
+    Effective genome size: 1870000000
+    Normalize profile: true
   outputs:
     MultiQC webpage:
       asserts:
         - that: "has_text"
           text: "wt_H3K4me3"
         - that: "has_text"
-          text: <a href="#cutadapt_filtered_reads" class="nav-l2">Filtered Reads</a>
+          text: <a href="#fastp" class="nav-l1">fastp</a>
         - that: "has_text"
           text: <a href="#bowtie2" class="nav-l1">Bowtie 2 / HiSAT2</a>
     'MultiQC on input dataset(s): Stats':
       asserts:
         has_line:
-          line: "Sample	macs2-d	macs2-treatment_redundant_rate	macs2-peak_count	bowtie_2_hisat2-overall_alignment_rate	cutadapt-percent_trimmed"
+          line: "Sample	macs2-d	macs2-treatment_redundant_rate	macs2-peak_count	bowtie_2_hisat2-overall_alignment_rate	fastp-pct_duplication	fastp-after_filtering_q30_rate	fastp-after_filtering_q30_bases	fastp-filtering_result_passed_filter_reads	fastp-after_filtering_gc_content	fastp-pct_surviving	fastp-pct_adapter"
         has_text_matching:
-          expression: "wt_H3K4me3\t201.0\t0.0\t11\t98.[0-9]*\t10.[0-9]*"
+          expression: "wt_H3K4me3\t20[12].0\t0.0\t13\t98.[0-9]*\t0.002\t93.[0-9]*\t4.5[0-9]*\t0.095[0-9]*\t57.[0-9]*\t95.[0-9]*\t0.19[0-9]*"
     filtered BAM:
       element_tests:
         wt_H3K4me3:
           asserts:
             has_size:
-              value: 5008461
-              delta: 200000
+              value: 5311841
+              delta: 500000
     MACS2 summits:
       element_tests:
         wt_H3K4me3:
           asserts:
             has_n_lines:
-              n: 11
+              n: 13
     MACS2 peaks:
       element_tests:
         wt_H3K4me3:
           asserts:
             - that: "has_text"
               text: "# effective genome size = 1.87e+09"
+            - that: "has_text_matching"
+              expression: "# fragment size is determined as 20[12] bps"
             - that: "has_text"
-              text: "# fragment size is determined as 201 bps"
-            - that: "has_text"
-              text: "# fragments after filtering in treatment: 41724"
+              text: "# fragments after filtering in treatment: 42745"
     MACS2 narrowPeak:
       element_tests:
         wt_H3K4me3:
           asserts:
             has_n_lines: 
-              n: 11
+              n: 13
     MACS2 report:
       element_tests:
         wt_H3K4me3:
           asserts:
             - that: "has_text"
               text: "# effective genome size = 1.87e+09"
+            - that: "has_text_matching"
+              expression: "# fragment size is determined as 20[12] bps"
             - that: "has_text"
-              text: "# fragment size is determined as 201 bps"
-            - that: "has_text"
-              text: "# fragments after filtering in treatment: 41724"
+              text: "# fragments after filtering in treatment: 42745"
     coverage from MACS2:
       element_tests:
         wt_H3K4me3:
            asserts:
               has_size:
-                value: 556477
-                delta: 10000
+                value: 568174
+                delta: 50000
     mapping stats:
       element_tests:
         wt_H3K4me3:
             asserts:
             - that: "has_text"
-              text: "1292 (2.79%) aligned concordantly 0 times"
+              text: "1344 (2.82%) aligned concordantly 0 times"
             - that: "has_text"
-              text: "39329 (84.93%) aligned concordantly exactly 1 time"
+              text: "42961 (90.29%) aligned concordantly exactly 1 time"
             - that: "has_text"
-              text: "5686 (12.28%) aligned concordantly >1 times"
+              text: "3276 (6.89%) aligned concordantly >1 times"