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sorry to bother, especially since I didn’t contrib...
# createpanelrefs
f
sorry to bother, especially since I didn’t contribute much lately.. I’m using this to create a mutect2 PoN for a panel and I’m having some issues with an error I can’t really trace on the code.. I’m using reference GRCh37 and it seems to point correctly to the s3 bucket in the log
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Apr-09 09:37:11.270 [PathVisitor-1] DEBUG nextflow.file.FileHelper - Started plugin 'nf-amazon' required to handle file: <s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh37/Sequence/W>
holeGenomeFasta/human_g1k_v37_decoy.dict
however, I get this soon after the pipeline starts
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Apr-09 09:37:11.899 [Actor Thread 10] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /temp/work/collect-file/ac7857958b3c7c78be84751d0b5539d7
Apr-09 09:37:11.909 [Actor Thread 10] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-17793772414752879742
Apr-09 09:37:12.064 [Actor Thread 12] ERROR nextflow.extension.OperatorImpl - @unknown
groovy.lang.MissingMethodException: No signature of method: Script_8d8ea946af003a8c$_runScript_closure1$_closure2$_closure6.call() is applicable for argument types: (LinkedList) values
: [[[id:null], /ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict]]
and this tuple here looks a little strange
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[[[id:null], /ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict]]
if it refers to this line, unless I’m wrong https://github.com/nf-core/createpanelrefs/blob/e6575b762ebf42950ce609d3e7ae954b19062c94/workflows/createpanelrefs.nf#L32 the 
[id:dict.baseName]
shouldn’t be null unless something happened, and I don’t see the 
s3://
part in the tuple but I’m not sure if that’s normal. would you have any clue which might point me in the right direction for debugging? (I’m using 
--tools mutect2
and my sample sheet is 
sample,cram,crai
) on google cloud
m
you're using the latest dev?
And no worries, we're getting close to a release, so any comment is a good comment
f
yeah, I’ve run with 
-r dev
so I’d guess latest merged on dev. but happy to try a specific commit point if you prefer
just make sure I’ve tested it with the references on one of my google buckets, and the error is the same (so at least I can exclude google vs amazon something)
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ERROR ~ Invalid method invocation `call` with arguments: [[id:null], /igenomes/references/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict] (java.util.LinkedList) on _closure6 type
(also in this case it’s cut 
gs://
)
m
can you try 
-r dev -latest
just to be sure
f
sure I’ll do straight away
same error, but the message
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N E X T F L O W   ~  version 24.10.5

Pulling nf-core/createpanelrefs ...
 Already-up-to-date
would highlight I already used the latest one
the log doesn’t help (me at least) to understand what’s happening, but I’m happy to debug as you wish
full launch was (barred privacy names)
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nextflow run nf-core/createpanelrefs -r dev -latest \
-c ../xxxxxx.config \
--input ../controls_crams_for_pon.csv \
--tools mutect2 \
--genome 'GATK.GRCh37' \
--outdir <gs://xxxxx/zzzzz/pon_data> \
--igenomes_base '<gs://xxxxx-references/igenomes/references>'
✅ 1
m
ok, good news
Let me see if I can try to reproduce then
so just a regular samplesheet and grch37
f
yep
samplesheet is in the form 
sample,cram,crai
r
Are you able to run the test profile @Francesco Lescai?
f
I’ll have to check, I’ve destroyed the VM now. didn’t tested that because it wasn’t the first time I used the pipeline
I’ll be able to get back to it tomorrow morning and I’ll let you know
m
I'm adding more tests to ensure we catch more scenario
@Ram I managed to solve the issues with your cnvkit PR
r
Sounds good Francesco!
Thanks @Maxime Garcia!
🎉 1
m
Good news, I reproduced the issue
a fix is incoming
f
oh yeah?! you’re an angel ☺️ I’m curious! what was the issue?
m
I'm thinking just that we only tested mutect2 with bam files and not cram files
ok actually no, what I thought was your issue is not, I'll continue investigating more
👀 1
Could you share .nextflow.log and content of xxxxxx.config?
f
I’ll send the config in a private message, and I’ll generate the log again on Monday morning (I’ve destroyed the VM)
🙏 1
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