A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Still getting an issue with `CHUNK_CLUSTERS` - even when running with a larger input file [thread]

Copied over the sample data from here:
<https://raw.githubusercontent.com/nf-core/test-datasets/proteinfamilies/test_data/mgnifams_input_small.fa>

to a local file `mgnifams_input_small.fa`:
```❯ head mgnifams_input_small.fa
&gt;1186628997
ILPLWVNTPGNNDACFGFSNIENDLNTICGEVQSIGQNNTFRILTSPYITLTPNLPKYNQTNINNITLTIPNSPVEKDYDISEYVNAINLSMQNIDALNTTTIYDVGSTELPDGSIAFIRDNTFHLFLDINKNFNEGMFEMDLTGSILFDSINGLLLNGANGNNILTDLSQIYASTIQGGKPITIGVNQHICKIMPKWDGVTPVVNGNEYDDPFDITFGNTESKTYINYFEFQNDINNIFSNYIDPISGLHILEGTL
&gt;6309221327
RLHPLEAISLEGPGINHTLRAQHVAERIAAILADETTTVYDRHLERHRPIRGLDSAILGLTHMLLKCYADALRELGIRARLAQDGWFMSREVQLAYHGLSFVADPQDRHAALYLAVTELGGDDLTSAVRTLLEGDDFSLPLLERLKDLSRRQGDRTVDELVAETLDAMALFDHAALWPEAG
&gt;2371018260_1_166
MNRLVSTLTAARIYELKRDFRKAAFYARLARQHAAEIGDPLLLAGAESTQGTLLAVDSRFEEAAECYRRALEVSAPPARVSALARALWQDNLGYCLIALDRTSEGLPLVHDALETIERAGATAHTVFPLMDLCFGYLKGDRYEEARYFGEACLERAPLCGDDSVER
&gt;1105114012
MVDVVVERGRITRLGPNAGAEAARAERAQVVDAAGRWVLPAFVDLFYPNDHGGGARDINPNGPDWSYKRFVQDNDAALGLTVELLSKSPCWRDTVIFVVEDDTQNGLDHVNGHRSLFLAISPWVKREAVTKRHLSLASVFKTIDLIFGLPPLNQYDAAASDLWD
&gt;1054961354
MPVYPYSNVKYKTLNKNELVKLIRKITVAWEKKTGRNQDLSLDRLKEETIPELKKHMKWYTSKDAAKNWEEWSGPSESATLYKVDEQRKGNDGNIWAVTQDKNGRKKWVLSMIHEGDNSYVSKSPKQNKFADSSEPVPIYSDSEDSERASSDDDLSESGLFPITSKSPKSKSNKKCQEGMLMNAATGKCRKNCAFHGMVRHRGSTRCSKKLEKCPPGQTRDSNSKKCRKPLKCPKGHRKDSETGECIKYTDTKEFKELNNDIDDDTQLSELSSDSGSDSGAVSGSESNLPRTPNNPESDLSESNLSSDISETPSNNENDSLDSKFKALLEEVLDYYKRTQGKIKFELVNSHTNRQNFIN
❯ grep '&gt;' mgnifams_input_small.fa | wc -l
   50000```

Have a local input file `samplesheet.csv`
```❯ cat samplesheet.csv
sample,fasta,existing_hmms_to_update,existing_msas_to_update
mgnifams_test,mgnifams_input_small.fa,,```

adjust the requirements to allow for local processing:
```❯ cat nextflow.config
process {
    resourceLimits = [
        cpus: 4,
        memory: '15.GB',
        time: '1.h'
    ]
}```

then run:
```❯ nextflow run nf-core/proteinfamilies --input samplesheet.csv --outdir ./protfam_test -profile docker -resume```

which generates the error:
```ERROR ~ Error executing process &gt; 'NFCORE_PROTEINFAMILIES:PROTEINFAMILIES:CHUNK_CLUSTERS (mgnifams_test)'

Caused by:
  Missing output file(s) `chunked_fasta/*` expected by process `NFCORE_PROTEINFAMILIES:PROTEINFAMILIES:CHUNK_CLUSTERS (mgnifams_test)````

Note: everything still works when I add the `test` profile, however I assume this isn’t meant to be left in for “production” runs?

We did a huddle for these. If you have any more concerns, poke me!