Hello again, similar error was discussed previously, but I'm unable to determine the cause in this case.

ERROR ~ Cannot get property 'baseName' on null object

 -- Check script '/cfs/klemming/projects/snic/sllstore2017078/lech/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/main.nf' at line: 133 or see '.nextflow.log' file for more details
ERROR ~ Cannot get property 'baseName' on null object

 -- Check script '/cfs/klemming/projects/snic/sllstore2017078/lech/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/main.nf' at line: 134 or see '.nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details

referred lines 133-135:

dbsnp.map{ it -> [[id:it[0].baseName], it] },
            dbsnp_tbi.map{ it -> [[id:it[0].baseName], it] },
            intervals)

my command:

nextflow run /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/sarek \
    -profile pdc_kth \
    -name $1 \
    -params-file /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/$2 \
    --project=${COMPUTE_ACCOUNT} \
    --email=${USER_E_MAIL} \
    --step prepare_recalibration \
    --known_snps /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz \
    --known_snps_tbi /cfs/klemming/projects/snic/sllstore2017078/lech/sarek/run1_no_GATK/get_known_sites_vcf/id_04.germline.pass.intersected.vcf.gz.tbi

json:

{
  "input": "/cfs/klemming/projects/snic/sllstore2017078/lech/sarek/sample_tables/atac_bams_for_sarek_1samp.csv",
  "outdir": "/cfs/klemming/projects/supr/sllstore2017078/lech/sarek/ail_recal_test1",
  "genome": "",
  "no_intervals": false,
  "tools": "deepvariant,freebayes,strelka,haplotypecaller",
  "concatenate_vcfs": true,
  "joint_germline": true,
  "save_output_as_bam": true,
  "known_indels_vqsr": false,
  "known_snps_vqsr": false,
  "ngscheckmate_bed": false,
  "use_gatk_spark": "baserecalibrator",
  "fasta": "/cfs/klemming/projects/snic/sllstore2017078/lech/sarek/refs/112/genome/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna_sm.toplevel.fa",
  "igenomes_ignore": true
}

This was recently fixed: https://github.com/nf-core/sarek/pull/1628/files are you on the latest release?

I cloned the repo last week, but the fix is not yet included in the stable release. Many thanks, this was obviously very helpful :)

ok but you are on the latest? looking into cutting a patch release with this in

Dumb question, but how do I check that? I pulled v3.4.3 master branch.

if you add

-r 3.4.3

it should make sure you are on a fixed revision. it is also reported in the

multiqc

report, the execution htmls and the

.nextflow.log

on startup

I was using a local copy now (AFAIC -r can't be use with local copies). But I'm pretty sure I was seeing this error with 3.4.3 revision, and I'm seeing it now with very recently cloned pipeline, albeit master branch. If I'm confusing something, just please specify what you mean, not being difficult, just learning ;)

no sounds right. didn't consider you were offline. in any case should be reported in the log file 🙂

The dev branch version, on which I run the most recent run went through without errors (run with the same input files) 👍