## cannot find nf-functions.nf module

[EorgeKit]

I managed to fix issue no #3 and #4 but then a new error came up , which happens even when I use conda as profile

The error is :

nextflow run main_AMR++.nf -profile singularity --pipeline demo
N E X T F L O W  ~  version 22.10.1
Launching `main_AMR++.nf` [insane_goodall] DSL2 - revision: 531e9acfee
 A M R + +    N F   P I P E L I N E
 ===================================
 reads        : /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/data/raw/*_R{1,2}.fastq.gz
 output       : test_results

Unable to read script: '/srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/../modules/Trimming/trimmomatic.nf' 
-- cause: 
Can't find a matching module file for include: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/modules/nf-functions.nf

[EorgeKit]

I managed to find the module from the bin file and relocate it to the modules directory.

The new error is :

nextflow run main_AMR++.nf -profile singularity --pipeline multiqc
N E X T F L O W  ~  version 22.10.1
Launching `main_AMR++.nf` [lonely_baekeland] DSL2 - revision: 531e9acfee
 A M R + +    N F   P I P E L I N E
 ===================================
 reads        : /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/data/raw/*_R{1,2}.fastq.gz
 output       : test_results

WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /srv/data/my_shared_data_folder/amrcattle/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
ERROR ################################################################
Please choose a pipeline!!!

To test the pipeline, use the "demo" pipeline :

ERROR ################################################################

I don't know much about the repeated processes stuff but the pipeline option I am sure its not working for some reason, I have tried with multiqc pipeline and the same error keeps popping up.

[EnriqueDoster]

@EorgeKit , thank you for pointing this out. We've made a few changes to AMR++ that should hopefully address those warnings that you are reporting. Please try the latest updates and let us know if you run into any further issues. Thanks!