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Updating workflows/genome_annotation/lncRNAs-annotation from 0.1 to 0.2#1253

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Updating workflows/genome_annotation/lncRNAs-annotation from 0.1 to 0.2#1253
gxydevbot wants to merge 1 commit into
galaxyproject:mainfrom
planemo-autoupdate:workflows/genome_annotation/lncRNAs-annotation

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@gxydevbot

@gxydevbot gxydevbot commented Jun 8, 2026

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Hello! This is an automated update of the following workflow: workflows/genome_annotation/lncRNAs-annotation. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

  • toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/3.0.3+galaxy1

The workflow release number has been updated from 0.1 to 0.2.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

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github-actions Bot commented Jun 8, 2026

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Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 0
Failure 1
Skipped 0
Failed Tests
  • ❌ Galaxy-Workflow-lncRNAs_annotation_workflow.ga_0

    Problems:

    • Output with path /tmp/tmpb3j4c73s/StringTie on dataset 2 and 3 Assembled transcripts__2c8ed41e-c024-4a05-b11c-283152038ec6.gtf different than expected
Expected 77365+-0 lines in the output found 78999

    • Output with path /tmp/tmphu5v81lo/lncRNA annotation with FEELnc on dataset 1, 5, and 6__35ee4409-2803-43d5-aa0e-c45e81612631.gtf different than expected
Expected 233+-0 lines in the output found 244

    • Output with path /tmp/tmp_mkangm2/Classifier output with FEELnc on dataset 1, 5, and 6__e88f01a6-d652-442d-950b-d2ed3d3709cf.txt different than expected
Expected 696+-0 lines in the output found 725

    • Output with path /tmp/tmp6f5ogvki/Concatenate multiple datasets or collections on dataset 5 and 7__34162119-e926-4a1b-b9e6-07c66524d15a.gtf different than expected
Expected 137681+-0 lines in the output found 137692

    Workflow invocation details

    • Invocation Messages

    • Steps

      • Step 1: strandedness:

        • step_state: scheduled

      • Step 2: Genome assembly:

        • step_state: scheduled

      • Step 3: Genome annotation:

        • step_state: scheduled

      • Step 4: Alignments from RNA-seq:

        • step_state: scheduled

      • Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • cd ../; python _evaluate_expression_.py

            Exit Code:

            • 0

            Traceback:

            • 

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d7c0cdfa632a11f19fe17ced8de37c25"

              

              
chromInfo
"/tmp/tmpfip1juvb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_param_type
{"__current_case__": 0, "input_param": "unstranded", "mappings": [{"__index__": 0, "from": "stranded - forward", "to": "--fr"}, {"__index__": 1, "from": "stranded - reverse", "to": "--rf"}, {"__index__": 2, "from": "unstranded", "to": ""}], "type": "text"}

              

              
output_param_type
"text"

              

              
unmapped
{"__current_case__": 1, "on_unmapped": "fail"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 6: gffread (toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/gffread:0.12.7--h077b44d_6
              

              • 

            

            Command Line:
            

              

            • 

              gffread '/tmp/tmpfip1juvb/files/b/4/5/dataset_b4535f33-1d52-4623-969c-b3aac76c4226.dat'       -T -o output.gtf
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d7c0cdfa632a11f19fe17ced8de37c25"

              

              
chr_replace
None

              

              
chromInfo
"/tmp/tmpfip1juvb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
decode_url
false

              

              
expose
false

              

              
filtering
None

              

              
full_gff_attribute_preservation
false

              

              
gffs
{"__current_case__": 2, "gff_fmt": "gtf", "tname": ""}

              

              
maxintron
None

              

              
merging
{"__current_case__": 0, "merge_sel": "none"}

              

              
reference_genome
{"__current_case__": 0, "source": "none"}

              

              
region
{"__current_case__": 0, "region_filter": "none"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 7: Assembly step with StringTie (toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/3.0.3+galaxy1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/mulled-v2-704aee0c18e3278557ac3bedcbb7986e3913f703:4d702b8c3ad3ff53c6023de86a21af7cf31defda-0
              

              • 

            

            Command Line:
            

              

            • 

              mkdir -p ./special_de_output/sample1/ &&   ln -s '/tmp/tmpfip1juvb/files/b/4/5/dataset_b4535f33-1d52-4623-969c-b3aac76c4226.dat' guide.gff &&  stringtie '/tmp/tmpfip1juvb/files/9/8/2/dataset_98269c8c-ffce-4d18-b358-23f1dc0a8caf.dat'  -o '/tmp/tmpfip1juvb/job_working_directory/000/6/outputs/dataset_2c8ed41e-c024-4a05-b11c-283152038ec6.dat' -p "${GALAXY_SLOTS:-1}"      -G guide.gff  -b ./special_de_output/sample1/  -f '0.01' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d7c0cdfa632a11f19fe17ced8de37c25"

              

              
adv
{"abundance_estimation": false, "bdist": "50", "bundle_fraction": "1.0", "disable_trimming": false, "fraction": "0.01", "min_anchor_cov": "1", "min_anchor_len": "10", "min_bundle_cov": "1", "min_tlen": "200", "multi_mapping": false, "name_prefix": null, "omit_sequences": "", "point_features": null}

              

              
chromInfo
"/tmp/tmpfip1juvb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
guide
{"__current_case__": 1, "coverage_file": false, "guide_source": {"__current_case__": 1, "guide_gff_select": "history", "ref_hist": {"values": [{"id": 2, "src": "hda"}]}}, "input_estimation": false, "special_outputs": {"__current_case__": 2, "special_outputs_select": "no"}, "use_guide": "yes"}

              

              
input_options
{"__current_case__": 0, "input_bam": {"values": [{"id": 3, "src": "hda"}]}, "input_mode": "short_reads"}

              

              
nascent_mode
""

              

              
rna_strandness
""

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 8: lncRNA annotation step with FEELnc (toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2.1+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/feelnc:0.2--pl526_0
              

              • 

            

            Command Line:
            

              

            • 

              export FEELNCPATH=$(dirname $(command -v FEELnc_pipeline.sh))/../ && ln -s '/tmp/tmpfip1juvb/files/8/f/a/dataset_8fa4b662-1cee-4e8e-957b-b278bc954487.dat' genome_fa && FEELnc_pipeline.sh --candidate='/tmp/tmpfip1juvb/files/2/c/8/dataset_2c8ed41e-c024-4a05-b11c-283152038ec6.dat' --reference='/tmp/tmpfip1juvb/files/9/a/4/dataset_9a4f23ec-6745-4613-8c95-3056d8771b21.dat' --genome=genome_fa --outname='candidate_lncRNA' --outdir='out_feelnc'  &&  cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Filtered transcripts will be available in file: 'out_feelnc/filter/candidate_lncRNA.filter.log'
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	Your input GTF file 'candidate_lncRNA.filter.gtf' contains *118* transcripts
	Extracting ORFs/cDNAs 1/118...
	Extracting ORFs/cDNAs 2/118...
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	Extracting ORFs/cDNAs 111/118...
	Extracted '111' ORF/cDNAs sequences on '118'.
> Run random Forest on '/tmp//439_candidate_lncRNA.codpot.test_rna.fa'
	1. Compute the size of each sequence and ORF
	2. Compute the kmer ratio for each kmer and put the output file name in a list
	3. Compute the kmer score for each kmer size on learning and test ORF
	4. Merge the score and size files into one file for each type
	5. Make the model on learning sequences and apply it on test sequences
		Running 10-fold cross-validation on learning

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  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
		10-fold cross-validation step is finish. Best threshold found: '0.6356'.
		Write the coding label for '439_candidate_lncRNA.codpot.modelTest.out' in 'out_feelnc/codpot//candidate_lncRNA.codpot_RF.txt'.
> Writing the GTF output files

Transcripts without ORF found: check file 'out_feelnc/codpot//candidate_lncRNA.codpot.noORF.gtf'.
	These transcripts correspond probably to lncRNAs since no ORF was found. You might also want to change the --testorftype option.
window : 10000 - max window : 100000 - lncrna : out_feelnc/codpot//candidate_lncRNA.codpot.lncRNA.gtf - mrna : /tmp/tmpfip1juvb/files/9/a/4/dataset_9a4f23ec-6745-4613-8c95-3056d8771b21.dat - biotype: 0
Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
 Importation  merge GTF file : 111 lncRNA done 
 Importation  merge GTF file : 13795 mRNA done 

              

              • 

            

            Standard Output:
            

              

            • 

              ####################
Create output directory out_feelnc

####################
Step 1/3: Running the FEELnc filter module:

commande line:
	FEELnc_filter.pl --infile=/tmp/tmpfip1juvb/files/2/c/8/dataset_2c8ed41e-c024-4a05-b11c-283152038ec6.dat --mRNAfile=/tmp/tmpfip1juvb/files/9/a/4/dataset_9a4f23ec-6745-4613-8c95-3056d8771b21.dat --biotype=transcript_biotype=protein_coding --monoex=-1 --outlog=out_feelnc/filter/candidate_lncRNA.filter.log > out_feelnc/filter/candidate_lncRNA.filter.gtf


####################
Step 2/3: Running the FEELnc codpot module:

commande line:
	FEELnc_codpot.pl --infile=out_feelnc/filter/candidate_lncRNA.filter.gtf --mRNAfile=/tmp/tmpfip1juvb/files/9/a/4/dataset_9a4f23ec-6745-4613-8c95-3056d8771b21.dat --genome=genome_fa -b transcript_biotype=protein_coding --mode=shuffle --outname=candidate_lncRNA.codpot --outdir=out_feelnc/codpot/


####################
Step 3/3: Running the FEELnc classifier module:

commande line:
	FEELnc_classifier.pl --lncrna=out_feelnc/codpot//candidate_lncRNA.codpot.lncRNA.gtf --mrna=/tmp/tmpfip1juvb/files/9/a/4/dataset_9a4f23ec-6745-4613-8c95-3056d8771b21.dat --log=out_feelnc/classifier/candidate_lncRNA.classifier.log > out_feelnc/classifier/candidate_lncRNA.classifier.txt



####################
Done: results in out_feelnc/{filter;codpot;classifier}

# Summary file:
-With_cutoff:	0.6356
-Nb_lncRNAs:	111
-Nb_mRNAs:	NA
#FEELnc Classification
#lncRNA file :  lncrna : out_feelnc/codpot//candidate_lncRNA.codpot.lncRNA.gtf 
#mRNA file : /tmp/tmpfip1juvb/files/9/a/4/dataset_9a4f23ec-6745-4613-8c95-3056d8771b21.dat
#Minimal window size : 10000
#Maximal window size : 100000
#Number of lncRNA : 111 
#Number of mRNA : 13795
#Number of interaction : 724 
#Number of lncRNA without interaction : 0
#List of lncRNA without interaction : 

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d7c0cdfa632a11f19fe17ced8de37c25"

              

              
chromInfo
"/tmp/tmpfip1juvb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 9: Concatenation step (cat1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/coreutils:8.31--h14c3975_0
              

              • 

            

            Command Line:
            

              

            • 

              cat '/tmp/tmpfip1juvb/files/9/a/4/dataset_9a4f23ec-6745-4613-8c95-3056d8771b21.dat' '/tmp/tmpfip1juvb/files/3/5/e/dataset_35ee4409-2803-43d5-aa0e-c45e81612631.dat' > '/tmp/tmpfip1juvb/job_working_directory/000/8/outputs/dataset_34162119-e926-4a1b-b9e6-07c66524d15a.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d7c0cdfa632a11f19fe17ced8de37c25"

              

              
chromInfo
"/tmp/tmpfip1juvb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
queries
[{"__index__": 0, "input2": {"values": [{"id": 7, "src": "hda"}]}}]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      
 
      

      • 

    • 

      Other invocation details

        

      • 

        history_id
        

          

        • 2f8f829aa67beebc
          • 

        

        • 

      • 

        history_state
        

          

        • ok
          • 

        

        • 

      • 

        invocation_id
        

          

        • 2f8f829aa67beebc
          • 

        

        • 

      • 

        invocation_state
        

          

        • scheduled
          • 

        

        • 

      • 

        workflow_id
        

          

        • 2f8f829aa67beebc
          • 

        

        • 

      

      

      • 

    
  
    

    • 





      		
    

  





        


            

            
            

              
            

        

      


      

            
  
  

    
  
    
    

  

  

  


    
















  
  

    

      

  










  








  
      

  
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