Version history

Pipeline Updates

  • Updated template to nf-core/tools v2.8
  • Add --bamqc_regions_file parameter for targeted methylation sequencing data #302
  • โœจ Add NF-TEST tests and snapshots for the pipeline test profile #310

Bug fixes & refactoring

  • ๐Ÿ› ๏ธ update index file channels to explicit value channels #310
  • ๐Ÿ› fix params.test_data_base in test and test_full configs #310
  • ๐Ÿค– GitHub Actions CI - pull_reqest to dev tests with NXF_VER latest-everything #310
  • ๐Ÿค– GitHub Actions CI - pull_reqest to master tests with NXF_VER 22.10.1 & latest-everything #310
  • ๐Ÿค– GitHub Actions CI - fail-fast set to false #310
  • ๐Ÿ› get to the bottom of index tests #278
  • โœจ Support for Bismark methylation extraction ignore and ignore_3prime parameters when ignore_r1 or ignore_3prime_r1 are greater than 0. #322
  • ๐Ÿ› ๏ธ rename ignore -> ignore_r1 and ignore_3prime -> ignore_3prime_r1 params #322
  • ๐Ÿ› removed unused directory #297

Pipeline Updates

  • โš™๏ธ Dramatically increase the default process time config requests for Bismark and bwa meth alignment
  • โœจ Add a tower.yml file to enable Reports in Nextflow Tower
  • ๐Ÿค– GitHub Actions CI - download the test data prior to running tests

Bug fixes & refactoring

  • ๐Ÿงน Refactor genome indices preparation into a separate workflow
  • ๐Ÿงน Refactor subworkflow logic out of alignment subworkflows, for later sharing
  • ๐Ÿ› Fix a bug with using a local genome reference FASTA file
  • ๐Ÿ› Fix a bunch of problems in the CI tests using nf-test (#279)

Pipeline Updates

  • โœจ Updated the bismark2summary step so that it no longer stages the aligned BAM files into the working directory (#268)
    • Should be much faster / cheaper for running on the cloud
  • โœจ Added ability to merge FastQ files based on shared IDs in sample sheet (#272)

Bug fixes & refactoring

  • ๐Ÿ› Fixed typo in parameter handling for input reference indices (#263)
  • ๐Ÿงน Removed orphaned --bismark_align_cpu_per_multicore and --bismark_align_cpu_per_multicore parameters.
    • Multi-core usage for Bismark alignment is now automatically set. If you would like to overwrite this, you can do so by setting ext.args for the process in a custom config.
  • ๐Ÿงน Removed duplicate option --coverage2cytosine (#273)
    • Use the existing option --cytosine_report to launch the new COVERAGE2CYTOSINE process.
    • Removed option --cytosine_report genome_index from the Bismark methylation extractor.

Pipeline Updates

  • โœจ Added option to run the Bismark coverage2cytosine script using the --coverage2cytosine and --nomeseq parameters.
  • ๐Ÿ› Fixed bad bug where trimming presets were not being applied (#261)

Software Updates

  • Update Bismark v0.23.0 to v0.24.0

Pipeline Updates

Major pipeline rewrite to use DSL2 with shared nf-core/modules.

Warning: Breaking change! โš ๏ธ

The pipeline now requires a sample sheet to be passed to the pipeline with --input:

samplefastq_1fastq_2genome

See an example here

Note: The genome column is not yet used but will give the ability to map to multiple genomes in a single run in a future release. See #181.

Supplying the reference geneome with --genome as before works as usual.

Software Updates

Major updates in commands and software versions for nearly every tool.

Please treat this new version with a little more care than usual and let us know if you find any problems!

Minor release to fix a bug in the command for the Bismark alignment. This change should have no effect on the pipeline output, though single-end alignments with Bismark should now be 2x faster. See issue #210 for full investigation.

Pipeline Updates

  • Added new config profile to run minimal test paired-end dataset, with -profile test_paired. Added to the CI tests.

Bug fixes

  • Fixed silent bug in Bismark alignment command that had no effect on the output (#210)

Software updates

  • Picard 2.25.1 > 2.25.4
  • MultiQC 1.10 > 1.10.1

โš ๏ธ Breaking change!

In line with a standardisation change across all of nf-core, we have changed the main parameter name for supplying files to the pipeline. In this release, please use --input instead of --reads. The parameter still works in the same way as before.

Pipeline Updates

  • Increased resources for fastqc process (#143)
  • Raised Nextflow version requirement to 20.07.1
  • Updated template to nf-core/tools 1.13.3
  • Renamed --reads to --input
  • Added new --maxins and --minins parameters to pass on to Bismark
  • New --em_seq preset
    • Sets bismark_maxins = 1000, clip_r1 = 8, clip_r2 = 8, three_prime_clip_r1 = 8, three_prime_clip_r2 = 8
  • New --publish_dir_mode parameter to customise results folder behaviour
  • Fix bug on AWS for bismark_hisat known splice file (#177)
  • Moved parameter documentation into new nextflow_schema.json file
  • Added a -profile test_full config for running the pipeline with a full-size test dataset
    • See the config file for details
    • This will be used for automated release tests on AWS, results browsable on the website

Software updates

  • Python base 3.7.3 > 3.8.8
  • markdown 3.1.1 > 3.3.4
  • pymdown-extensions 6.0 > 8.1.1
  • pygments 2.6.1 > 2.8.1
  • pigz 2.3.4 > 2.6
  • samtools 1.9 > 1.11
  • TrimGalore! 0.6.5 > 0.6.6
  • Bowtie2 2.3.5 > 2.4.2
  • Hisat2 2.2.0 > 2.2.1
  • Bismark 0.22.3 > 0.23.0
  • Picard 2.22.2 > 2.25.1
  • MethylDackel 0.5.0 > 0.5.2
  • MultiQC 1.8 > 1.10

New features

  • Added multicore support for TrimGalore!
  • Improved the multicore support for Bismark methXtract for more parallelisation (#121)
  • Added --cytosine_report option to tell Bismark to give reports for all cytosines in the genome.
  • Added options --bismark_align_cpu_per_multicore and --bismark_align_cpu_per_multicore to customise how Bismark align --multicore is decided (#124)

Software updates

  • New: pigz 2.3.4
  • Python base 2.7 > 3.7.3
  • FastQC 0.11.8 > 0.11.9
  • TrimGalore! 0.6.4 > 0.6.5
  • HiSAT2 2.1.0 > 2.2.0
  • Bismark 0.22.2 > 0.22.3
  • Qualimap 2.2.2c > 2.2.2d
  • Picard 2.21.3 > 2.22.2
  • MethylDackel 0.4.0 > 0.5.0
  • MultiQC 1.7 > 1.8

Pipeline Updates

  • Fixed bug where the iGenomes config was loaded after the references were set (#121)
  • Removed awsbatch config profile because it is now served by nf-core/configs
  • Tidied up the summary log messages when starting the pipeline
    • Fewer messages saying what youโ€™re not doing, sanitised the order of some logs and removed a few things
  • Slightly refactored the code for trimming parameters
  • Updated template to tools 1.9

Bug fixes

  • Fixed error where MethylDackel would consume the Nextflow channels and not work with more than one sample #140

New features

  • Changed all parameter names to snake_case
  • Added --local_alignment option to run Bismark with the --local flag to allow soft-clipping of reads.
  • Added support for bismarkโ€™s SLAM-seq mode
  • Added support for running bismark with HISAT2 as an aligner option #85
  • Added support for centralized configuration profiles nf-core/configs
  • Add --meth_cutoff parameter to change default for bismark_methylation_extractor
    • eg. use --meth_cutoff 5 on the command line or params.meth_cutoff = 5 to require 5 overlapping reads to call a methylation site.
  • Added --methyl_kit option to run MethylDackel with the --methylKit flag, producing output suitable for the methylKit R package.

Software updates

  • new dependency: hisat2 2.1.0
  • new dependency: r-markdown 1.1
  • TrimGalore! 0.5.0 > 0.6.4
  • Bismark 0.20.0 > 0.22.2
  • Bowtie2 2.3.4.3 > 2.3.5
  • Picard 2.18.21 > 2.21.3
  • Qualimap 2.2.2b > 2.2.2c
  • MethylDackel 0.3.0 > 0.4.0

Pipeline updates

  • Keep memory in GB for samtools, to avoid problems with unit conversion (#99)
  • Changed params.container for process.container
  • Synchronised with version 1.7 of the nf-core/tools template

Bug fixes

  • Fixed a bug that caused conda dependencies to be resolved very slowly
  • Allowed some spare memory in the samtools sort steps, avoiding crashes for some users (#81)

A fairly quick release on the heels of 1.2 to fix a nasty bug introduced that prevented the pipeline from running on more than one file. Whilst weโ€™re here we added in a new tool: preseq.

New features

  • Added preseq analysis to calculate sample complexity.
    • This new step can help decide sufficient sequencing depth has been reached.

Bug fixes

  • Fixed new bug that meant pipeline only worked with one sample at a time #66
    • Introduced in previous release. TrimGalore onwards would only process one sample.

New features

  • Trim 9bp from both ends of both reads for PBAT mode.
  • Save where_are_my_files.txt to results directory to inform the user about missing intermediate files (#42)

Software updates

  • Fastqc 0.11.7 > 0.11.8
  • Bowtie2 2.3.4.2 > 2.3.4.3
  • Bismark 0.19.1 > 0.20.0
  • Qualimap 2.2.2a > 2.2.2b
  • Picard 2.18.11 > 2.18.21
  • MultiQC 1.6 > 1.7

Bug fixes

  • Fixed error when running the pipeline with --unmapped
    • Previously, could result in error Error ~ No such variable: bismark_unmapped
  • Fixed error where single-sample reports could mix up log files (#48)
  • Fixed bug in MultiQC process that skipped results from some tools
  • Supply available memory as argument to Picard MarkDuplicates

  • Tests simplified - now work by simply using the test config profile
    • eg: nextflow run nf-core/methylseq -profile test,docker
    • Removed previous run_test.sh script and data
  • New Singularity build script for direct compatibility with singularity-hub
  • Minor improvements to the docs
  • A number of boilerplate nf-core code updates
  • Updated process$name nextflow syntax to avoid warnings in new versions of nextflow
  • Updated software tools
    • trim-galore v0.4.5 update to 0.5.0
    • samtools v1.8 update to 1.9
    • bowtie2 v2.3.4.1 update to 2.3.4.2
    • multiqc v1.5 update to 1.6
    • picard v2.18.2 update to 2.18.11
    • bwameth v0.2.0 update to 0.2.2

First release of this pipeline under the nf-core flag. It also marks a significant step up in the maturity of the workflow, with everything now in a single script and both aligner workflows fully supported.

  • Renamed and moved SciLifeLab/NGI-MethylSeq to nf-core/methylseq
  • Merged bwa-meth and bismark pipeline scripts, now chosen with --aligner flag
  • Refactored multi-core parameters for Bismark alignment and methylation extraction
  • Rewrote most of the documentation
  • Changed the Docker container to use Bioconda installations

For earlier releases and development notes, please see the (now archived) fork at SciLifeLab/NGI-MethylSeq.