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nf-core/airrflow: nf-core/airrflow version 2.1.0 "Accio"

Gisela Gabernet; Susanna; Alexander Peltzer; David Ladd; nf-core bot; Simon Heumos; Maxime U. Garcia; Josef; Phil Ewels; Kevin Menden

Main new features
  • Added possibility of processing BCR / TCR amplicon data without UMI barcodes.
  • Sample sheet now follows the AIRR standard.
  • Added option to skip clustering sequences according to similarity (pRESTO ClusterSets).
Added
  • #130: Organized presto processes in presto_umi subworkflow.
  • #128: Added presto_sans_umi subworkflow option. Added postassembly FastQC and corresponding section in MultiQC. Included refs for analysis of light chains (if present) by default.
  • updated docs for --library_generation_method parameter.
  • Samplesheet column names were updated to follow the AIRR standard.
  • Fixed docs on --umi_start parameter, this parameter should only be used when UMIs are provided in the index reads.
  • #143 Template update to nf-core tools v2.2.
  • #150 Added option to search for reverse primers.
  • #159 Template update to nf-core tools v2.3.1, v2.3.1
  • #161 Add option to skip clustering sequences in the UMI workflow
  • #163 Added process labels and software version emitting to all modules. Fixed output folder name for changeo processes.
  • Bump versions to 2.1.0
Fixed
  • #150: Fixed cprimer start position, when cprimer in R2 reads.
  • Remove need for a plot when Hamming threshold cannot be generated.
  • The shazam threshold process is not executed when the hamming threshold is provided.
  • #164: Fixed AWS tests when running on fusion mounts, solving #137.
Dependencies
Dependency Old version New version

| igblast | 1.15.0 | 1.17.1 | | presto | 0.6.2 | 0.7.0 | | changeo | 1.0.2 | 1.2.0 | | r-base | 4.0.3 | 4.1.2 | | r-alakazam | 1.0.2 | 1.2.0 | | r-shazam | 0.1.11 | 1.1.0 | | r-tigger | 0.3.1 | 1.0.0 |

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. NB: Dependency has been removed if new version information isn't present.

Deprecated
  • Parameter --protocol was updated to --library_generation_method to follow the AIRR standard.
  • Parameter --loci and --species were converted to a column in the samplesheet (pcr_target_locus and species) to allow processing simultaneously TR and IG loci from the same sample, also allow processing different species in one samplesheet.
  • Removed genotyping step with tiGGer.
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nf-core/airrflow-2.1.0.zip
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