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

• 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).

• #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

• #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.

| 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.

• 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.