How to run / startup failed

[olgabot]

Hello,
I'm trying to run this pipeline on data from this paper and am not sure how to get started. What is the syntax for specifying the reads, genome, transcriptome, etc? I tried nextflow run biocorecrg/indrop to get help and the build failed (below).
Can you help me understand what may be happening?
Warmest,
Olga

 Mon  4 Mar - 10:26  ~/code/indrop   origin ☊ master ✔ 
  nextflow run biocorecrg/indrop
N E X T F L O W  ~  version 19.01.0
Pulling biocorecrg/indrop ...
 downloaded from https://github.com/biocorecrg/indrop.git
Launching `biocorecrg/indrop` [stupefied_joliot] - revision: 89fce82042 [master]
ERROR ~ unable to resolve class QualityChecker
 @ line 111, column 14.
       def qc = new QualityChecker(input:read, cpus:task.cpus)
                ^

_nf_script_3de07612: 159: unable to resolve class QualityChecker
 @ line 159, column 14.
       def qc = new QualityChecker(input:filtered_read, cpus:task.cpus)
                ^

_nf_script_3de07612: 179: unable to resolve class QualityChecker
 @ line 179, column 14.
       def qc = new QualityChecker(input:right_pair)
                ^

_nf_script_3de07612: 203: unable to resolve class NGSaligner
 @ line 203, column 19.
       def aligner = new NGSaligner(reference_file:genomeFile, index:"STARgenome", annotation_file:annotationFile, read_size:read_size-1, cpus:task.cpus)
                     ^

_nf_script_3de07612: 226: unable to resolve class NGSaligner
 @ line 226, column 19.
       def aligner = new NGSaligner(id:pair_id, reads:reads, index:STARgenome, cpus:task.cpus, output:"STAR_${pair_id}")
                     ^

5 errors


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

[lucacozzuto]

Dear Olga, did you follow the Readme? You should install the library by running sh INSTALL.sh and have either singularity or docker installed in your system. Let me know if it works.

Best,

Luca

[lucacozzuto]

Hi Olga, I need to document more the pipeline. (I'm still writing it). The parameters are specified in the parameters file and the adapters in the corresponding config file in the config folder. Best, Luca Il lun 4 mar 2019, 19:37 Olga Botvinnik <notifications@github.com> ha scritto:

…

Hello, I'm trying to run this pipeline on data from this paper <https://jasn.asnjournals.org/content/29/8/2069> and am not sure how to get started. What is the syntax for specifying the reads, genome, transcriptome, etc? I tried nextflow run biocorecrg/indrop to get help and the build failed (below). Can you help me understand what may be happening? Warmest, Olga Mon 4 Mar - 10:26  ~/code/indrop   origin ☊ master ✔   nextflow run biocorecrg/indrop N E X T F L O W ~ version 19.01.0 Pulling biocorecrg/indrop ... downloaded from https://github.com/biocorecrg/indrop.git Launching `biocorecrg/indrop` [stupefied_joliot] - revision: 89fce82 [master] ERROR ~ unable to resolve class QualityChecker @ line 111, column 14. def qc = new QualityChecker(input:read, cpus:task.cpus) ^ _nf_script_3de07612: 159: unable to resolve class QualityChecker @ line 159, column 14. def qc = new QualityChecker(input:filtered_read, cpus:task.cpus) ^ _nf_script_3de07612: 179: unable to resolve class QualityChecker @ line 179, column 14. def qc = new QualityChecker(input:right_pair) ^ _nf_script_3de07612: 203: unable to resolve class NGSaligner @ line 203, column 19. def aligner = new NGSaligner(reference_file:genomeFile, index:"STARgenome", annotation_file:annotationFile, read_size:read_size-1, cpus:task.cpus) ^ _nf_script_3de07612: 226: unable to resolve class NGSaligner @ line 226, column 19. def aligner = new NGSaligner(id:pair_id, reads:reads, index:STARgenome, cpus:task.cpus, output:"STAR_${pair_id}") ^ 5 errors -- Check '.nextflow.log' file for details — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APPSvYIuHUx-FR7BdHQN5wDUg1J7OaTpks5vTWfYgaJpZM4bc9RA> .

[olgabot]

Thank you for your response! Yes, I was able to follow the INSTALL.sh, I'm just confused at what to do next, what flags are required, whether they can be AWS S3 paths or do they all need to be local, etc

[lucacozzuto]

Hi Olga, I tested this on HPC cluster but not in the cloud. It should be possible to run in the cloud since Nextflow supports this... The required parameters are in params.config while in nextflow.config are specified the resources needed.