Add BISCUIT

.github/workflows/ci.yml

@@ -21,14 +21,16 @@ jobs:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
         nxf_ver: ['20.04.0', '']
-        aligner: ['bismark', 'bismark_hisat', 'bwameth']
+        aligner: ['bismark', 'bismark_hisat', 'bwameth', 'biscuit']
         include:
           - aligner: 'bismark'
             ref_index: --bismark_index results/reference_genome/BismarkIndex/
           - aligner: 'bismark_hisat'
             ref_index: --bismark_index results/reference_genome/BismarkIndex/
           - aligner: 'bwameth'
             ref_index: --bwa_meth_index results/reference_genome/genome.fa
+          - aligner: 'biscuit'
+            ref_index: --bwa_biscuit_index results/reference_genome/genome.fa
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2

CHANGELOG.md

@@ -1,3 +1,4 @@
+
 # nf-core/methylseq
 
 ## v1.6dev - [date]
@@ -22,9 +23,18 @@ The parameter still works in the same way as before.
 * Added a `-profile test_full` config for running the pipeline with a full-size test dataset
   * See [the config file](https://github.com/nf-core/methylseq/blob/dev/conf/test_full.config) for details
   * This will be used for automated release tests on AWS, results browsable on the website
+* Added Picard CollectInsertSizeMetrics and Picard CollectGcBiasMetrics
+* Improved qulimap and preseq by adding `samtools sort` and `samtools index` step in the Bismark aligner
+* Added BISCUIT aligner as an optional aligner, with all relative steps (alignment, mark duplicates with [samblaster](https://github.com/GregoryFaust/samblaster), methylation extraction, QC for biscuit, and optional [Epi-read](https://huishenlab.github.io/biscuit/epiread_format/) file creation with SNP information ).
 
 ### Software updates
 
+* _new_: samblaster `0.1.26`
+* _new_: bedtools `2.30.0`
+* _new_: biscuit `0.3.16.20200420`
+* _new_: bcftools`1.10`
+* _new_: parallel `20201122`
+* _new_: gawk `5.1.0`
 * Python base `3.7.3` > `3.8.5`
 * markdown `3.1.1` > `3.3.3`
 * pymdown-extensions `6.0` > `8.1.1`

README.md

@@ -16,21 +16,22 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 ## Pipeline Summary
 
 The pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark) or [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel).
-Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`.
-
-| Step                                         | Bismark workflow | bwa-meth workflow     |
-|----------------------------------------------|------------------|-----------------------|
-| Generate Reference Genome Index _(optional)_ | Bismark          | bwa-meth              |
-| Raw data QC                                  | FastQC           | FastQC                |
-| Adapter sequence trimming                    | Trim Galore!     | Trim Galore!          |
-| Align Reads                                  | Bismark          | bwa-meth              |
-| Deduplicate Alignments                       | Bismark          | Picard MarkDuplicates |
-| Extract methylation calls                    | Bismark          | MethylDackel          |
-| Sample report                                | Bismark          | -                     |
-| Summary Report                               | Bismark          | -                     |
-| Alignment QC                                 | Qualimap         | Qualimap              |
-| Sample complexity                            | Preseq           | Preseq                |
-| Project Report                               | MultiQC          | MultiQC               |
+Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth` or `--aligner biscuit`.
+
+| Step                                         | Bismark workflow | bwa-meth workflow     | biscuit           |
+|----------------------------------------------|------------------|-----------------------|-------------------|
+| Generate Reference Genome Index _(optional)_ | Bismark          | bwa-meth              | biscuit           |
+| Raw data QC                                  | FastQC           | FastQC                | FastQC            |
+| Adapter sequence trimming                    | Trim Galore!     | Trim Galore!          | Trim Galore!      |
+| Align Reads                                  | Bismark          | bwa-meth              | biscuit           |
+| Deduplicate Alignments                       | Bismark          | Picard MarkDuplicates | samblaster        |
+| Extract methylation calls                    | Bismark          | MethylDackel          | biscuit           |
+| Sample Report                                | Bismark          | -                     | biscuit QC        |
+| Summary Report                               | Bismark          | -                     | -                 |
+| Picard Metrics                               | Picard           | Picard                | Picard            |
+| Alignment QC                                 | Qualimap         | Qualimap              | Qualimap          |
+| Sample complexity                            | Preseq           | Preseq                | Preseq            |
+| Project Report                               | MultiQC          | MultiQC               | MultiQC           |
 
 ## Quick Start
 

assets/common_dbsnp.hdr

@@ -0,0 +1,11 @@
+##INFO=<ID=TYPE,Number=1,Type=String,Description="Variation class/type snv">
+##INFO=<ID=COMMON_SOME,Number=1,Type=Integer,Description="1 percent common in some of the population sources in UCSC">
+##INFO=<ID=COMMON_ALL,Number=1,Type=Integer,Description="1 percent common in all of the available population sources in UCSC">
+##INFO=<ID=REF_MIN,Number=.,Type=Character,Description="ref genotype, less ambiguous from dbsnp or other sources">
+##INFO=<ID=ALT_MIN,Number=.,Type=Character,Description="alt genotype, less ambiguous from dbsnp or other sources">
+##INFO=<ID=REF_DBSNP,Number=.,Type=Character,Description="ref genotype, dbSNP">
+##INFO=<ID=ALT_DBSNP,Number=.,Type=Character,Description="alt genotype, dbSNP">
+##INFO=<ID=REF_ALL,Number=.,Type=Character,Description="ref genotype, other sources">
+##INFO=<ID=ALT_ALL,Number=.,Type=Character,Description="alt genotype, other sources">
+##INFO=<ID=MAX_MAF,Number=.,Type=Float,Description="maximum minor allele frequency among all sources">
+##INFO=<ID=RSID,Number=1,Type=String,Description="dbsnp ID">