cwl: Source 'outputtbi' of type ["null", "File"] may be incompatible

Question

[lizhichao]

Hi,i write a workflow ,but it report errors： cwl: Source 'outputtbi' of type ["null", "File"] may be incompatible i dont konw whats meaning？

[ATpoint]

lizhichao, please do not constantly add content via the Answer box which is reserved for answers. Best would be to use edit in order to put additional information in the toplevel question. That way you avoid a messy thread.

[lizhichao]

OK. I will pay attention to it . I have solve the problem .the reason is cwl workflow Strictly requires the file types of the nodes before and after to be consistent

[lizhichao]

Hi,i write a workflow ,but it report errors olympus.cwl:173:9: Source 'outputtbi' of type ["null", "File"] may be incompatible

[lizhichao]

errors：Workflow checker warning: olympus.cwl:173:9: Source 'outputtbi' of type ["null", "File"] may be incompatible olympus.cwl:262:9: with sink 'intbi' of type ["null", {"items": "File", "type": "array"}] olympus.cwl:214:9: Source 'outputbam' of type ["null", "File"] may be incompatible olympus.cwl:224:9: with sink 'inbam' of type "File" Tool definition failed validation: olympus.cwl:10:5: Source 'fastq1' of type "File" is incompatible olympus.cwl:91:9: with sink 'fastq1' of type "File" source has linkMerge method merge_flattened olympus.cwl:26:5: Source 'fastq2' of type ["null", "File"] is incompatible olympus.cwl:105:9: with sink 'fastq2' of type ["null", "File"] source has linkMerge method merge_flattened olympus.cwl:172:9: Source 'outputvcf' of type ["null", "File"] is incompatible olympus.cwl:250:9: with sink 'invcf' of type {"items": "File", "inputBinding": {"prefix": "-V", "separate": true}, "type": "array"} olympus.cwl:240:9: Source 'outputvcf' of type ["null", "File"] is incompatible olympus.cwl:158:9: with sink 'ingvcf' of type {"items": "File", "inputBinding": {"prefix": "-V", "separate": true}, "type": "array"} olympus.cwl:241:9: Source 'outtbi' of type ["null", "File"] is incompatible olympus.cwl:168:9: with sink 'intbi' of type {"items": "File", "type": "array"}

enter code here

[lizhichao]

my cwl :class: Workflow cwlVersion: v1.0 id: olympus doc: basic olympus wgs pipeline label: olympus $namespaces: sbg: 'https://www.sevenbridges.com/' inputs: - id: fastq1 type: File 'sbg:x': -552.9009399414062 'sbg:y': 181.4827117919922 - id: ref type: 'File[]' 'sbg:x': -366.6666564941406 'sbg:y': -274.69183349609375 - id: runnable type: File 'sbg:x': 64.8259048461914 'sbg:y': -491.0832824707031 - id: yaml type: File 'sbg:x': -353.3706970214844 'sbg:y': -120.35742950439453 - id: fastq2 type: File? 'sbg:x': -545.9559936523438 'sbg:y': -10.20911979675293 - id: bundle type: 'File[]' 'sbg:x': -554.97412109375 'sbg:y': -152.34645080566406 outputs: - id: clean_check outputSource: - soapnuke/clean_check type: 'File[]' 'sbg:x': -115.54717254638672 'sbg:y': 249.7547149658203 - id: base outputSource: - soapnuke/base type: 'File[]' 'sbg:x': -173 'sbg:y': 349 - id: qual outputSource: - soapnuke/qual type: 'File[]' 'sbg:x': 126.943115234375 'sbg:y': -70.5 - id: stat outputSource: - soapnuke/stat type: 'File[]' 'sbg:x': -62.056884765625 'sbg:y': -147.5 - id: outputvcf_1 outputSource: - GenotypeGVCFs/outputvcf type: File? 'sbg:x': 702.496826171875 'sbg:y': -13.597484588623047 - id: tranches outputSource: - vqsr/tranches type: 'File[]?' 'sbg:x': 1217.607421875 'sbg:y': -2.5437231063842773 - id: rscriptFile outputSource: - vqsr/rscriptFile type: 'File[]?' 'sbg:x': 1465.6263427734375 'sbg:y': 314.61981201171875 - id: recal outputSource: - vqsr/recal type: 'File[]?' 'sbg:x': 1274.7269287109375 'sbg:y': 491.9908752441406 - id: outputvcf outputSource: - vqsr/outputvcf type: File? 'sbg:x': 1163.8974609375 'sbg:y': 667.6852416992188 steps: - id: soapnuke in: - id: fastq1 linkMerge: merge_flattened source: - fastq1 - id: adapter3 default: AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA - id: adapter5 default: AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG - id: findNtile default: '''True''' - id: seqType default: '''2''' - id: opt_cut default: 0 - id: fastq2 linkMerge: merge_flattened source: - fastq2 - id: low_qual_rate default: 12 - id: n_rate default: 0.1 - id: raw_qual_system default: '''True''' - id: clean_qual_system default: '''True''' - id: remove_index default: '''False''' - id: trim_head_tail default: '0,0,0,0' - id: read_id default: '''0''' - id: outType default: '''0''' - id: cutAdaptor default: 0 - id: misMatch default: 2 - id: prefix default: NA12878 out: - id: clean_fqs - id: clean_check - id: qual - id: base - id: stat run: ./soapnuke.cwl label: soapnuke 'sbg:x': -307.7547302246094 'sbg:y': 121.91194915771484 - id: markdup in: - id: inbam source: - bwa/outbam - id: outbam default: NA12878.markdup.bam out: - id: outputbam run: ./markdup.cwl label: markdup 'sbg:x': -20.55974769592285 'sbg:y': 132.20755004882812

[Tom]

Hi!

I am sure there is an easy fix for this. Please post your workflow and tool (olympus.cwl). I see that you have already posted the workflow below, but i'm not willing to try and decipher it as long as it doesn't have any line breaks.

General Answer: The type of the item your workflow is trying to feed into the tool doesn't match the type that is specified in the inputs section of the tool. The tool expects an array of files while the workflow only provides a single file.

Regards, Tom

Answer 1

[lizhichao]

I have solve the problem .the reason is cwl workflow Strictly requires the file types of the nodes before and after to be consistent. Thank you anyway！