Hey #CE8SSJV3N and #C0493FQQZ3P, Has anyone able to use more than one

nf-core

pipelines without any technical issues, like this one:

Starting Nextflow pipeline...                                                                                                                     [95/1969]

 N E X T F L O W ~ version 24.04.4

Launching `<https://github.com/nf-core/rnasplice>` [confident_wozniak] DSL2 - revision: 1d0494ae34 [1.0.4]

WARN: Access to undefined parameter `bbsplit_index` -- Initialise it to a default value eg. `params.bbsplit_index = some_value`
WARN: Access to undefined parameter `kallisto_index` -- Initialise it to a default value eg. `params.kallisto_index = some_value`
WARN: Access to undefined parameter `rsem_index` -- Initialise it to a default value eg. `params.rsem_index = some_value`
WARN: Access to undefined parameter `hisat2_index` -- Initialise it to a default value eg. `params.hisat2_index = some_value`
WARN: Access to undefined parameter `additional_fasta` -- Initialise it to a default value eg. `params.additional_fasta = some_value`
WARN: Access to undefined parameter `gene_bed` -- Initialise it to a default value eg. `params.gene_bed = some_value`
WARN: The following invalid input values have been detected:

* --contrasts: /home/tud03125/pipeline/contrast_NORMAL.csv
* --source: fastq
* --clip_r1: null
* --clip_r2: null
* --three_prime_clip_r1: null
* --three_prime_clip_r2: null
* --trim_nextseq: null
* --skip_trimgalore_fastqc: false
* --rmats: true
* --rmats_splice_diff_cutoff: 0.0001
* --rmats_paired_stats: true
* --rmats_read_len: 40
* --rmats_novel_splice_site: false
* --rmats_min_intron_len: 50
* --rmats_max_exon_len: 500
* --dexseq_exon: true
* --save_dexseq_annotation: false
* --gff_dexseq: null
* --alignment_quality: 10
* --aggregation: true
* --save_dexseq_plot: true
* --n_dexseq_plot: 10
* --edger_exon: true
* --save_edger_plot: true
* --n_edger_plot: 10
* --dexseq_dtu: true
* --dtu_txi: dtuScaledTPM
* --sashimi_plot: true
* --miso_genes: ENSG00000004961, ENSG00000005302, ENSG00000147403
* --miso_genes_file: null
* --miso_read_len: 75
* --fig_width: 7
* --fig_height: 7                                                                                                                                 [49/1969]
* --min_samps_feature_expr: 2
* --min_samps_feature_prop: 2
* --min_samps_gene_expr: 4
* --min_feature_expr: 10
* --min_feature_prop: 0.1
* --min_gene_expr: 10
* --suppa: true
* --suppa_per_local_event: true
* --suppa_per_isoform: true
* --suppa_tpm: null
* --generateevents_pool_genes: true
* --generateevents_event_type: SE SS MX RI FL
* --generateevents_boundary: S
* --generateevents_threshold: 10
* --generateevents_exon_length: 100
* --psiperevent_total_filter: 0
* --diffsplice_local_event: true
* --diffsplice_isoform: true
* --diffsplice_method: empirical
* --diffsplice_area: 1000
* --diffsplice_lower_bound: 0
* --diffsplice_gene_correction: true
* --diffsplice_paired: true
* --diffsplice_alpha: 0.05
* --diffsplice_median: false
* --diffsplice_tpm_threshold: 0
* --diffsplice_nan_threshold: 0
* --clusterevents_local_event: true
* --clusterevents_isoform: true
* --clusterevents_sigthreshold: null
* --clusterevents_dpsithreshold: 0.05
* --clusterevents_eps: 0.05
* --clusterevents_metric: euclidean
* --clusterevents_separation: null
* --clusterevents_min_pts: 20
* --clusterevents_method: DBSCAN                                                                                                                  [13/1969]




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                                      ,--./,-.
      ___   __ __ __ ___   /,-._.--~'
 |\ | |__ __ / ` / \ |__) |__       } {
 | \| |     \__, \__/ | \ |___   \`-._,-`-,
                                      `._,._,'
 nf-core/rnaseq v3.14.0-g1d0494a
------------------------------------------------------
Core Nextflow options
 revision            : 1.0.4
 runName             : confident_wozniak
 containerEngine     : singularity
 launchDir           : /home/tud03125/pipeline
 workDir             : /home/tud03125/pipeline/normal_human_liver_rnasplice_2/work
 projectDir          : /home/tud03125/.nextflow/assets/nf-core/rnasplice
 userName            : tud03125
 profile             : singularity
 configFiles         :

Input/output options
 input               : /home/tud03125/pipeline/normal_human_liver_design_rnasplice_2.csv
 outdir              : /home/tud03125/pipeline/normal_human_liver_rnasplice_2

Reference genome options
 fasta               : /home/tud03125/pipeline/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
 gtf                 : /home/tud03125/pipeline/Homo_sapiens.GRCh38.108.gtf
 star_index          : /home/tud03125/STAR_index
 salmon_index        : /home/tud03125/salmon_index

Read filtering options
 ribo_database_manifest: /home/tud03125/ribo_database_manifest.txt

Alignment options
 min_mapped_reads    : 5

Optional outputs
 save_reference      : true

Quality Control
 rseqc_modules       : bam_stat, inner_distance, infer_experiment, junction_annotation, junction_saturation, read_distribution, read_duplication

!! Only displaying parameters that differ from the pipeline defaults !!

This was a while ago for me. But, one of my issues with

nf-core/rnasplice

was that it got mixed up with my

nf-core/rnaseq

pipeline too, giving me 1) these list of warnings (that should’ve been in

nf-core/rnaseq

and not in

nf-core/rnasplice

), and 2) these mix-ups in the title page:

nf-core/rnaseq v3.14.0-g1d0494a

and

revision: 1.0.4

. Because of that, GitHub gave me this suggestion: “I’d recommend uninstalling both workflows and then running the rnasplice test suite on your HPC to see if that resolves the issue. You can do this with the following command…” Doing that worked well. But, I don't want to have to constantly uninstall one in order to properly use the other, especially if I want to run

nf-core/rnaseq

and

nf-core/rnasplice

pipelines at the same time (one with PBS job, and another with Unix's multiplexer like

tmux

or

screen

). So, I was wondering if you can have more than one, different

nf-core

pipelines inside the HPC cluster, or did you have to constantly uninstall one and then install the other one (like uninstall

nf-core/rnaseq

in order to install

nf-core/rnasplice

properly, without any mistaken screw-ups)?

Sorry, I'm confused. The two pipeline should be installed in different directories, completely separate from each other. And they should also be run in different directories, otherwise the

.nextflow.log

files and the caches (in

.nextflow

by default) will get into each other's way.