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nf-core / tools

Python package with helper tools for the nf-core community.
https://nf-co.re
MIT License
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nf-core website API results response not recognised #2373

Closed paoloAngelino closed 1 year ago

paoloAngelino commented 1 year ago

Description of the bug

When selecting the web based launch method, I get the following error: ERROR nf-core website API results response not recognised: https://nf-co.re/launch See verbose log for full response

Command used and terminal output

nf-core -v launch rnaseq -r 3.12.0

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.9 - https://nf-co.re

DEBUG    Fetching list of nf-core workflows                                                                                                       list.py:102
INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config files or profiles                               launch.py:137

DEBUG    Guessed nextflow assets directory - pulling pipeline dirnames                                                                            list.py:123
DEBUG    Fetching extra info about 3 local workflows                                                                                              list.py:139
DEBUG    Guessed nextflow assets workflow directory: /home/aguerradesouza/.nextflow/assets/nf-core/chipseq                                        list.py:339
DEBUG    Pulling git info from /home/aguerradesouza/.nextflow/assets/nf-core/chipseq                                                              list.py:353
DEBUG    Popen(['git', 'cat-file', '--batch-check'], cwd=/home/aguerradesouza/.nextflow/assets/nf-core/chipseq, universal_newlines=False,          cmd.py:976
         shell=None, istream=<valid stream>)
DEBUG    Guessed nextflow assets workflow directory: /home/aguerradesouza/.nextflow/assets/nf-core/fetchngs                                       list.py:339
DEBUG    Pulling git info from /home/aguerradesouza/.nextflow/assets/nf-core/fetchngs                                                             list.py:353
DEBUG    Popen(['git', 'cat-file', '--batch-check'], cwd=/home/aguerradesouza/.nextflow/assets/nf-core/fetchngs, universal_newlines=False,         cmd.py:976
         shell=None, istream=<valid stream>)
DEBUG    Guessed nextflow assets workflow directory: /home/aguerradesouza/.nextflow/assets/nf-core/rnaseq                                         list.py:339
DEBUG    Pulling git info from /home/aguerradesouza/.nextflow/assets/nf-core/rnaseq                                                               list.py:353
DEBUG    Popen(['git', 'cat-file', '--batch-check'], cwd=/home/aguerradesouza/.nextflow/assets/nf-core/rnaseq, universal_newlines=False,           cmd.py:976
         shell=None, istream=<valid stream>)
INFO     Using local workflow: nf-core/rnaseq (v3.12.0)                                                                                            list.py:62
DEBUG    JSON file loaded: /home/aguerradesouza/.nextflow/assets/nf-core/rnaseq/nextflow_schema.json                                            schema.py:114
DEBUG    JSON Schema Draft7 validated                                                                                                           schema.py:344
INFO     [✓] Default parameters match schema validation                                                                                         schema.py:246
DEBUG    Collecting pipeline parameter defaults                                                                                                 schema.py:656

DEBUG    Got '/home/aguerradesouza/.nextflow/assets/nf-core/rnaseq' as path                                                                      utils.py:228
DEBUG    Found a config cache, loading: /home/aguerradesouza/.nextflow/nf-core/wf-config-cache-fff322b7a0d125b35c1b4ea2e.json                    utils.py:262
DEBUG    Skipped following pipeline params because they had nested parameter values:                                                            schema.py:671
         params.genomes.GRCh37.fasta, params.genomes.GRCh37.bwa, params.genomes.GRCh37.bowtie2, params.genomes.GRCh37.star,
         params.genomes.GRCh37.bismark, params.genomes.GRCh37.gtf, params.genomes.GRCh37.bed12, params.genomes.GRCh37.readme,
         params.genomes.GRCh37.mito_name, params.genomes.GRCh37.macs_gsize, params.genomes.GRCh37.blacklist, params.genomes.GRCh38.fasta,
         params.genomes.GRCh38.bwa, params.genomes.GRCh38.bowtie2, params.genomes.GRCh38.star, params.genomes.GRCh38.bismark,
         params.genomes.GRCh38.gtf, params.genomes.GRCh38.bed12, params.genomes.GRCh38.mito_name, params.genomes.GRCh38.macs_gsize,
         params.genomes.GRCh38.blacklist, params.genomes.CHM13.fasta, params.genomes.CHM13.bwa, params.genomes.CHM13.bwamem2,
         params.genomes.CHM13.gtf, params.genomes.CHM13.gff, params.genomes.CHM13.mito_name, params.genomes.GRCm38.fasta,
         params.genomes.GRCm38.bwa, params.genomes.GRCm38.bowtie2, params.genomes.GRCm38.star, params.genomes.GRCm38.bismark,
         params.genomes.GRCm38.gtf, params.genomes.GRCm38.bed12, params.genomes.GRCm38.readme, params.genomes.GRCm38.mito_name,
         params.genomes.GRCm38.macs_gsize, params.genomes.GRCm38.blacklist, params.genomes.TAIR10.fasta, params.genomes.TAIR10.bwa,
         params.genomes.TAIR10.bowtie2, params.genomes.TAIR10.star, params.genomes.TAIR10.bismark, params.genomes.TAIR10.gtf,
         params.genomes.TAIR10.bed12, params.genomes.TAIR10.readme, params.genomes.TAIR10.mito_name, params.genomes.EB2.fasta,
         params.genomes.EB2.bwa, params.genomes.EB2.bowtie2, params.genomes.EB2.star, params.genomes.EB2.bismark, params.genomes.EB2.gtf,
         params.genomes.EB2.bed12, params.genomes.EB2.readme, params.genomes.'UMD3.1'.fasta, params.genomes.'UMD3.1'.bwa,
         params.genomes.'UMD3.1'.bowtie2, params.genomes.'UMD3.1'.star, params.genomes.'UMD3.1'.bismark, params.genomes.'UMD3.1'.gtf,
         params.genomes.'UMD3.1'.bed12, params.genomes.'UMD3.1'.readme, params.genomes.'UMD3.1'.mito_name, params.genomes.WBcel235.fasta,
         params.genomes.WBcel235.bwa, params.genomes.WBcel235.bowtie2, params.genomes.WBcel235.star, params.genomes.WBcel235.bismark,
         params.genomes.WBcel235.gtf, params.genomes.WBcel235.bed12, params.genomes.WBcel235.mito_name, params.genomes.WBcel235.macs_gsize,
         params.genomes.'CanFam3.1'.fasta, params.genomes.'CanFam3.1'.bwa, params.genomes.'CanFam3.1'.bowtie2, params.genomes.'CanFam3.1'.star,
         params.genomes.'CanFam3.1'.bismark, params.genomes.'CanFam3.1'.gtf, params.genomes.'CanFam3.1'.bed12,
         params.genomes.'CanFam3.1'.readme, params.genomes.'CanFam3.1'.mito_name, params.genomes.GRCz10.fasta, params.genomes.GRCz10.bwa,
         params.genomes.GRCz10.bowtie2, params.genomes.GRCz10.star, params.genomes.GRCz10.bismark, params.genomes.GRCz10.gtf,
         params.genomes.GRCz10.bed12, params.genomes.GRCz10.mito_name, params.genomes.BDGP6.fasta, params.genomes.BDGP6.bwa,
         params.genomes.BDGP6.bowtie2, params.genomes.BDGP6.star, params.genomes.BDGP6.bismark, params.genomes.BDGP6.gtf,
         params.genomes.BDGP6.bed12, params.genomes.BDGP6.mito_name, params.genomes.BDGP6.macs_gsize, params.genomes.EquCab2.fasta,
         params.genomes.EquCab2.bwa, params.genomes.EquCab2.bowtie2, params.genomes.EquCab2.star, params.genomes.EquCab2.bismark,
         params.genomes.EquCab2.gtf, params.genomes.EquCab2.bed12, params.genomes.EquCab2.readme, params.genomes.EquCab2.mito_name,
         params.genomes.EB1.fasta, params.genomes.EB1.bwa, params.genomes.EB1.bowtie2, params.genomes.EB1.star, params.genomes.EB1.bismark,
         params.genomes.EB1.gtf, params.genomes.EB1.bed12, params.genomes.EB1.readme, params.genomes.Galgal4.fasta, params.genomes.Galgal4.bwa,
         params.genomes.Galgal4.bowtie2, params.genomes.Galgal4.star, params.genomes.Galgal4.bismark, params.genomes.Galgal4.gtf,
         params.genomes.Galgal4.bed12, params.genomes.Galgal4.mito_name, params.genomes.Gm01.fasta, params.genomes.Gm01.bwa,
         params.genomes.Gm01.bowtie2, params.genomes.Gm01.star, params.genomes.Gm01.bismark, params.genomes.Gm01.gtf,
         params.genomes.Gm01.bed12, params.genomes.Gm01.readme, params.genomes.Mmul_1.fasta, params.genomes.Mmul_1.bwa,
         params.genomes.Mmul_1.bowtie2, params.genomes.Mmul_1.star, params.genomes.Mmul_1.bismark, params.genomes.Mmul_1.gtf,
         params.genomes.Mmul_1.bed12, params.genomes.Mmul_1.readme, params.genomes.Mmul_1.mito_name, params.genomes.'IRGSP-1.0'.fasta,
         params.genomes.'IRGSP-1.0'.bwa, params.genomes.'IRGSP-1.0'.bowtie2, params.genomes.'IRGSP-1.0'.star,
         params.genomes.'IRGSP-1.0'.bismark, params.genomes.'IRGSP-1.0'.gtf, params.genomes.'IRGSP-1.0'.bed12,
         params.genomes.'IRGSP-1.0'.mito_name, params.genomes.'CHIMP2.1.4'.fasta, params.genomes.'CHIMP2.1.4'.bwa,
         params.genomes.'CHIMP2.1.4'.bowtie2, params.genomes.'CHIMP2.1.4'.star, params.genomes.'CHIMP2.1.4'.bismark,
         params.genomes.'CHIMP2.1.4'.gtf, params.genomes.'CHIMP2.1.4'.bed12, params.genomes.'CHIMP2.1.4'.readme,
         params.genomes.'CHIMP2.1.4'.mito_name, params.genomes.'Rnor_5.0'.fasta, params.genomes.'Rnor_5.0'.bwa,
         params.genomes.'Rnor_5.0'.bowtie2, params.genomes.'Rnor_5.0'.star, params.genomes.'Rnor_5.0'.bismark, params.genomes.'Rnor_5.0'.gtf,
         params.genomes.'Rnor_5.0'.bed12, params.genomes.'Rnor_5.0'.mito_name, params.genomes.'Rnor_6.0'.fasta, params.genomes.'Rnor_6.0'.bwa,
         params.genomes.'Rnor_6.0'.bowtie2, params.genomes.'Rnor_6.0'.star, params.genomes.'Rnor_6.0'.bismark, params.genomes.'Rnor_6.0'.gtf,
         params.genomes.'Rnor_6.0'.bed12, params.genomes.'Rnor_6.0'.mito_name, params.genomes.'R64-1-1'.fasta, params.genomes.'R64-1-1'.bwa,
         params.genomes.'R64-1-1'.bowtie2, params.genomes.'R64-1-1'.star, params.genomes.'R64-1-1'.bismark, params.genomes.'R64-1-1'.gtf,
         params.genomes.'R64-1-1'.bed12, params.genomes.'R64-1-1'.mito_name, params.genomes.'R64-1-1'.macs_gsize, params.genomes.EF2.fasta,
         params.genomes.EF2.bwa, params.genomes.EF2.bowtie2, params.genomes.EF2.star, params.genomes.EF2.bismark, params.genomes.EF2.gtf,
         params.genomes.EF2.bed12, params.genomes.EF2.readme, params.genomes.EF2.mito_name, params.genomes.EF2.macs_gsize,
         params.genomes.Sbi1.fasta, params.genomes.Sbi1.bwa, params.genomes.Sbi1.bowtie2, params.genomes.Sbi1.star,
         params.genomes.Sbi1.bismark, params.genomes.Sbi1.gtf, params.genomes.Sbi1.bed12, params.genomes.Sbi1.readme,
         params.genomes.'Sscrofa10.2'.fasta, params.genomes.'Sscrofa10.2'.bwa, params.genomes.'Sscrofa10.2'.bowtie2,
         params.genomes.'Sscrofa10.2'.star, params.genomes.'Sscrofa10.2'.bismark, params.genomes.'Sscrofa10.2'.gtf,
         params.genomes.'Sscrofa10.2'.bed12, params.genomes.'Sscrofa10.2'.readme, params.genomes.'Sscrofa10.2'.mito_name,
         params.genomes.AGPv3.fasta, params.genomes.AGPv3.bwa, params.genomes.AGPv3.bowtie2, params.genomes.AGPv3.star,
         params.genomes.AGPv3.bismark, params.genomes.AGPv3.gtf, params.genomes.AGPv3.bed12, params.genomes.AGPv3.mito_name,
         params.genomes.hg38.fasta, params.genomes.hg38.bwa, params.genomes.hg38.bowtie2, params.genomes.hg38.star,
         params.genomes.hg38.bismark, params.genomes.hg38.gtf, params.genomes.hg38.bed12, params.genomes.hg38.mito_name,
         params.genomes.hg38.macs_gsize, params.genomes.hg38.blacklist, params.genomes.hg19.fasta, params.genomes.hg19.bwa,
         params.genomes.hg19.bowtie2, params.genomes.hg19.star, params.genomes.hg19.bismark, params.genomes.hg19.gtf,
         params.genomes.hg19.bed12, params.genomes.hg19.readme, params.genomes.hg19.mito_name, params.genomes.hg19.macs_gsize,
         params.genomes.hg19.blacklist, params.genomes.mm10.fasta, params.genomes.mm10.bwa, params.genomes.mm10.bowtie2,
         params.genomes.mm10.star, params.genomes.mm10.bismark, params.genomes.mm10.gtf, params.genomes.mm10.bed12, params.genomes.mm10.readme,
         params.genomes.mm10.mito_name, params.genomes.mm10.macs_gsize, params.genomes.mm10.blacklist, params.genomes.bosTau8.fasta,
         params.genomes.bosTau8.bwa, params.genomes.bosTau8.bowtie2, params.genomes.bosTau8.star, params.genomes.bosTau8.bismark,
         params.genomes.bosTau8.gtf, params.genomes.bosTau8.bed12, params.genomes.bosTau8.mito_name, params.genomes.ce10.fasta,
         params.genomes.ce10.bwa, params.genomes.ce10.bowtie2, params.genomes.ce10.star, params.genomes.ce10.bismark, params.genomes.ce10.gtf,
         params.genomes.ce10.bed12, params.genomes.ce10.readme, params.genomes.ce10.mito_name, params.genomes.ce10.macs_gsize,
         params.genomes.canFam3.fasta, params.genomes.canFam3.bwa, params.genomes.canFam3.bowtie2, params.genomes.canFam3.star,
         params.genomes.canFam3.bismark, params.genomes.canFam3.gtf, params.genomes.canFam3.bed12, params.genomes.canFam3.readme,
         params.genomes.canFam3.mito_name, params.genomes.danRer10.fasta, params.genomes.danRer10.bwa, params.genomes.danRer10.bowtie2,
         params.genomes.danRer10.star, params.genomes.danRer10.bismark, params.genomes.danRer10.gtf, params.genomes.danRer10.bed12,
         params.genomes.danRer10.mito_name, params.genomes.danRer10.macs_gsize, params.genomes.dm6.fasta, params.genomes.dm6.bwa,
         params.genomes.dm6.bowtie2, params.genomes.dm6.star, params.genomes.dm6.bismark, params.genomes.dm6.gtf, params.genomes.dm6.bed12,
         params.genomes.dm6.mito_name, params.genomes.dm6.macs_gsize, params.genomes.equCab2.fasta, params.genomes.equCab2.bwa,
         params.genomes.equCab2.bowtie2, params.genomes.equCab2.star, params.genomes.equCab2.bismark, params.genomes.equCab2.gtf,
         params.genomes.equCab2.bed12, params.genomes.equCab2.readme, params.genomes.equCab2.mito_name, params.genomes.galGal4.fasta,
         params.genomes.galGal4.bwa, params.genomes.galGal4.bowtie2, params.genomes.galGal4.star, params.genomes.galGal4.bismark,
         params.genomes.galGal4.gtf, params.genomes.galGal4.bed12, params.genomes.galGal4.readme, params.genomes.galGal4.mito_name,
         params.genomes.panTro4.fasta, params.genomes.panTro4.bwa, params.genomes.panTro4.bowtie2, params.genomes.panTro4.star,
         params.genomes.panTro4.bismark, params.genomes.panTro4.gtf, params.genomes.panTro4.bed12, params.genomes.panTro4.readme,
         params.genomes.panTro4.mito_name, params.genomes.rn6.fasta, params.genomes.rn6.bwa, params.genomes.rn6.bowtie2,
         params.genomes.rn6.star, params.genomes.rn6.bismark, params.genomes.rn6.gtf, params.genomes.rn6.bed12, params.genomes.rn6.mito_name,
         params.genomes.sacCer3.fasta, params.genomes.sacCer3.bwa, params.genomes.sacCer3.bowtie2, params.genomes.sacCer3.star,
         params.genomes.sacCer3.bismark, params.genomes.sacCer3.readme, params.genomes.sacCer3.mito_name, params.genomes.sacCer3.macs_gsize,
         params.genomes.susScr3.fasta, params.genomes.susScr3.bwa, params.genomes.susScr3.bowtie2, params.genomes.susScr3.star,
         params.genomes.susScr3.bismark, params.genomes.susScr3.gtf, params.genomes.susScr3.bed12, params.genomes.susScr3.readme,
         params.genomes.susScr3.mito_name
INFO     [✓] Pipeline schema looks valid (found 100 params)                                                                                      schema.py:98
INFO     Would you like to enter pipeline parameters using a web-based interface or a command-line wizard?                                      launch.py:279
DEBUG    Using selector: EpollSelector                                                                                                  selector_events.py:54
? Choose launch method Web based
DEBUG    Starting new HTTPS connection (1): nf-co.re:443                                                                               connectionpool.py:1048
DEBUG    https://nf-co.re:443 "POST /launch HTTP/1.1" 301 None                                                                          connectionpool.py:546
DEBUG    Starting new HTTPS connection (1): oldsite.nf-co.re:443                                                                       connectionpool.py:1048
DEBUG    https://oldsite.nf-co.re:443 "GET /launch/ HTTP/1.1" 301 239                                                                   connectionpool.py:546
DEBUG    Resetting dropped connection: oldsite.nf-co.re                                                                                 connectionpool.py:292
DEBUG    https://oldsite.nf-co.re:443 "GET /launch HTTP/1.1" 200 3218                                                                   connectionpool.py:546
DEBUG    Response content:                                                                                                                       utils.py:412
         b'<!doctype html>\n<html lang="en">\n\n<head>\n    <meta charset="utf-8">\n    <meta name="viewport" content="width=device-width,
         initial-scale=1, shrink-to-fit=no">\n    <meta name="color-scheme" content="light dark">\n    <!-- FontAwesome -->\n    <script
         src="https://kit.fontawesome.com/38356a05cc.js" crossorigin="anonymous"></script>\n    <!-- Global site tag (gtag.js) - Google
         Analytics -->\n    <script async src="https://www.googletagmanager.com/gtag/js?id=UA-68098153-2"></script>\n    <!-- Other JS -->\n
         <script src="/assets/lib/jquery.min.js"></script>\n    <script src="/assets/lib/bootstrap.bundle.min.js"></script>\n    <script
         src="/assets/lib/highlight.min.js"></script>\n    <script src="/assets/lib/groovy.min.js"></script>\n    <!-- Page-specific CSS and JS
         -->\n            <script src="/assets/lib/moment.js"></script>\n        <script src="/assets/lib/showdown.min.js"></script>\n
         <script src="/assets/js/nf-core-schema-launcher.js?c="></script>\n    \n    <!-- Custom nf-core CSS and JS -->\n    <link
         href="/assets/css/nf-core-dark.css?c=" rel="stylesheet" id="theme-stylesheet">\n    <script
         src="/assets/js/nf-core.js?c="></script>\n</head>\n\n<body tabindex="0">\n            <div class="mainpage">\n\n            \n
         \n    <div class="container main-content pt-5">\n        <p class="lead mt-5">This tool shows the available parameters for a pipeline
         in form for you to fill in.\n            It typically works in combination with the <a href="/tools"><code>nf-core</code> helper
         package</a>.\n        </p>\n\n        <h2>Launch a pipeline from the web</h2>\n\n        <p>Pick a pipeline and release below to show
         the launch form for that pipeline.\n            When you click <em>Finished</em>, your inputs will be saved and you\'ll be shown the
         commands\n            to use to launch the pipeline with your choices.</p>\n\n        <div class="card card-body mb-3">\n
         <form action="" method="get" class="d-flex flex-column flex-lg-row" id="launch_select_pipeline">\n                <div class="m-2
         my-lg-0 flex-fill">\n                    <div>\n                        <label for="launch-pipeline-name"
         class="d-lg-none">Pipeline:</label>\n                        <select class="form-select" name="pipeline" id="launch-pipeline-name">\n
         <option value="">Select a pipeline</option>\n                            <option value="">--</option>\n
         <option
         data-releases=\'["3.1.0","3.0","2.4.0","2.3.0","2.2.0","2.1.0","2.0.0","1.2.0","1.1.0","1.0.0","dev"]\'>airrflow</option><option
         data-releases=\'["2.6.1","2.6.0","2.5.0","2.4.1","2.4.0","2.3.2","2.3.1","2.3.0","2.2.0","2.1.1","2.1.0","2.0.0","1.2.0","1.1.3","1.1.2
         ","1.1.1","1.1.0","1.0.0","dev"]\'>ampliseq</option><option
         data-releases=\'["2.0","1.2.2","1.2.1","1.2.0","1.1.0","1.0.0","dev"]\'>atacseq</option><option
         data-releases=\'["2.0.0","1.1.1","1.1.0","1.0.0","dev"]\'>bacass</option><option
         data-releases=\'["1.0.0","dev"]\'>bactmap</option><option
         data-releases=\'["2.0.0","1.2.0","1.1.0","1.0.0","dev"]\'>bamtofastq</option><option
         data-releases=\'["1.0.2","1.0.1","1.0.0","dev"]\'>cageseq</option><option data-releases=\'["dev"]\'>callingcards</option><option
         data-releases=\'["2.0.0","1.2.2","1.2.1","1.2.0","1.1.0","1.0.0","dev"]\'>chipseq</option><option
         data-releases=\'["1.0.4","1.0.3","1.0.2","1.0.1","1.0.0","dev"]\'>circdna</option><option
         data-releases=\'["dev"]\'>circrna</option><option data-releases=\'["1.0.0","dev"]\'>clipseq</option><option
         data-releases=\'["1.1.1","1.1","1.0","dev"]\'>coproid</option><option data-releases=\'["dev"]\'>createpanelrefs</option><option
         data-releases=\'["2.0.0","1.0","dev"]\'>crisprseq</option><option
         data-releases=\'["3.1","3.0","2.0","1.1","1.0.0","dev"]\'>cutandrun</option><option
         data-releases=\'["1.3.2","1.3.1","1.3.0","1.2.0","1.1.0","1.0.0","dev"]\'>demultiplex</option><option
         data-releases=\'["1.2.4","1.2.3","1.2.2","1.2.1","1.2.0","1.1.0","1.0.0","dev"]\'>diaproteomics</option><option
         data-releases=\'["1.2.0","1.1.1","1.1.0","1.0.1","1.0.0","dev"]\'>differentialabundance</option><option
         data-releases=\'["1.0.0","dev"]\'>dualrnaseq</option><option
         data-releases=\'["2.4.7","2.4.6","2.4.5","2.4.4","2.4.3","2.4.2","2.4.1","2.4.0","2.3.5","2.3.4","2.3.3","2.3.2","2.3.1","2.3.0","2.2.2
         ","2.2.1","2.2.0","2.1.0","2.0.7","2.0.6","2.0.5","2.0.4","2.0.3","2.0.2","2.0.1","2.0.0","dev"]\'>eager</option><option
         data-releases=\'["2.2.1","2.2.0","2.1.0","2.0.0","1.1.0","1.0.0","dev"]\'>epitopeprediction</option><option
         data-releases=\'["dev"]\'>fastquorum</option><option
         data-releases=\'["1.10.0","1.9","1.8","1.7","1.6","1.5","1.4","1.3","1.2","1.1","1.0","dev"]\'>fetchngs</option><option
         data-releases=\'["1.1.2","1.1.1","1.1.0","1.0.1","1.0.0","dev"]\'>funcscan</option><option
         data-releases=\'["dev"]\'>genomeannotator</option><option data-releases=\'["dev"]\'>genomeassembler</option><option
         data-releases=\'["dev"]\'>gwas</option><option data-releases=\'["1.1.0","1.0.0","dev"]\'>hgtseq</option><option
         data-releases=\'["2.1.0","2.0.0","1.3.0","1.2.2","1.2.1","1.2.0","1.1.0","1.0.0","dev"]\'>hic</option><option
         data-releases=\'["1.0.0","dev"]\'>hicar</option><option
         data-releases=\'["2.0.0","1.2.0","1.1.5","1.1.4","1.1.3","1.1.2","1.1.1","1.1.0","1.0.0","dev"]\'>hlatyping</option><option
         data-releases=\'["1.0.0","dev"]\'>imcyto</option><option
         data-releases=\'["1.1.4","1.1.3","1.1.2","1.1.1","1.1.0","1.0.0","dev"]\'>isoseq</option><option
         data-releases=\'["dev"]\'>lncpipe</option><option
         data-releases=\'["2.3.2","2.3.1","2.3.0","2.2.1","2.2.0","2.1.1","2.1.0","2.0.0","1.2.0","1.1.2","1.1.1","1.1.0","1.0.0","dev"]\'>mag</
         option><option data-releases=\'["1.0.2","1.0.1","1.0.0","v0.1","dev"]\'>marsseq</option><option
         data-releases=\'["dev"]\'>mcmicro</option><option data-releases=\'["1.0.1","1.0.0","dev"]\'>metaboigniter</option><option
         data-releases=\'["dev"]\'>metapep</option><option data-releases=\'["dev"]\'>metatdenovo</option><option
         data-releases=\'["2.4.0","2.3.0","2.2.0","2.1.0","2.0.0","1.6.1","1.6","1.5","1.4","1.3","1.2","1.1","1.0","dev"]\'>methylseq</option><
         option
         data-releases=\'["2.4.1","2.4.0","2.3.1","2.3.0","2.2.0","2.1.0","2.0.0","1.6.0","1.5.1","1.5","1.4","1.3","1.2.6","1.2.5","1.2.4","1.2
         .3","1.2.2","1.2.1","1.2.0","1.1.0","1.0.0","dev"]\'>mhcquant</option><option
         data-releases=\'["1.0.0","dev"]\'>mnaseseq</option><option data-releases=\'["dev"]\'>molkart</option><option
         data-releases=\'["3.1.0","3.0.0","2.0.1","2.0.0","1.1.0","1.0.0","dev"]\'>nanoseq</option><option
         data-releases=\'["1.1.1","1.1.0","1.0.0","dev"]\'>nanostring</option><option
         data-releases=\'["2.1.1","2.1.0","2.0.0","1.0","dev"]\'>nascent</option><option data-releases=\'["dev"]\'>pangenome</option><option
         data-releases=\'["1.0.0","dev"]\'>pgdb</option><option data-releases=\'["1.0.0","dev"]\'>phyloplace</option><option
         data-releases=\'["1.0.0","dev"]\'>proteinfold</option><option data-releases=\'["1.0.0","dev"]\'>proteomicslfq</option><option
         data-releases=\'["1.1.1","1.1.0","1.0","dev"]\'>quantms</option><option data-releases=\'["dev"]\'>radseq</option><option
         data-releases=\'["1.0.0","dev"]\'>raredisease</option><option data-releases=\'["dev"]\'>rnadnavar</option><option
         data-releases=\'["2.3.4","2.3.3","2.3.2","2.3.1","2.3.0","2.2.0","2.1.0","2.0.0","1.2.0","1.1.0","1.0.2","1.0.1","1.0","dev"]\'>rnafusi
         on</option><option
         data-releases=\'["3.12.0","3.11.2","3.11.1","3.11.0","3.10.1","3.10","3.9","3.8.1","3.8","3.7","3.6","3.5","3.4","3.3","3.2","3.1","3.0
         ","2.0","1.4.2","1.4.1","1.4","1.3","1.2","1.1","1.0","dev"]\'>rnaseq</option><option
         data-releases=\'["dev"]\'>rnasplice</option><option data-releases=\'["1.0.0","dev"]\'>rnavar</option><option
         data-releases=\'["3.2.3","3.2.2","3.2.1","3.2.0","3.1.2","3.1.1","3.1","3.0.2","3.0.1","3.0","2.7.2","2.7.1","2.7","2.6.1","2.6","2.5.2
         ","2.5.1","2.5","dev"]\'>sarek</option><option data-releases=\'["dev"]\'>scflow</option><option
         data-releases=\'["2.3.2","2.3.1","2.3.0","2.2.0","2.1.0","2.0.0","1.1.0","1.0.0","dev"]\'>scrnaseq</option><option
         data-releases=\'["1.0.0","dev"]\'>slamseq</option><option
         data-releases=\'["2.2.1","2.2.0","2.1.0","2.0.0","1.1.0","1.0.0","dev"]\'>smrnaseq</option><option
         data-releases=\'["dev"]\'>spatialtranscriptomics</option><option data-releases=\'["dev"]\'>spinningjenny</option><option
         data-releases=\'["1.0.1","1.0.0","dev"]\'>taxprofiler</option><option data-releases=\'["dev"]\'>variantcatalogue</option><option
         data-releases=\'["0.1.0","dev"]\'>viralintegration</option><option
         data-releases=\'["2.6.0","2.5","2.4.1","2.4","2.3.1","2.3","2.2","2.1","2.0","1.1.0","1.0.0","dev"]\'>viralrecon</option><option
         data-releases=\'["dev"]\'>website</option>                        </select>\n                    </div>\n                </div>\n
         <div class="m-2 my-lg-0 flex-fill">\n                    <div>\n                        <label for="launch-pipeline-release"
         class="d-lg-none">Release:</label>\n                        <select class="form-select" name="release" id="launch-pipeline-release"
         disabled>\n                            <option>Pipeline release</option>\n                        </select>\n
         </div>\n                </div>\n                <div class="m-2 my-lg-0 ">\n                    <button type="submit" class="btn
         btn-primary btn-launch rocket-launch-hover" id="launch-pipeline-submit" disabled>\n                        <i class="fad
         fa-rocket"></i> Launch\n                    </button>\n                </div>\n            </form>\n        </div>\n\n        <p>For
         more options, such as launching a custom pipeline or using a GitHub branch, please use this tool locally - see below.</p>\n
         <p>Read more about the different nf-core pipelines on the <a href="/pipelines">Pipelines</a> page.</p>\n\n        <h2>Launch a pipeline
         locally</h2>\n\n        <p>You can run <code>nf-core launch</code> to submit any pipeline schema to this page and set the parameters
         required for launch.\n            This should work with any Nextflow pipeline (though the experience is best for pipelines that have a
         <code>nextflow_schema.json</code> file).</p>\n\n        <p>For example, to launch the <a href="/atacseq">nf-core/atacseq</a> pipeline
         in your current directory:</p>\n        <pre><code>nf-core launch atacseq</code></pre>\n\n        <p>To launch your own custom pipeline
         that you have locally:</p>\n        <pre><code>nf-core launch ./my_pipeline/</code></pre>\n\n        <p>The tool will check the
         pipeline\'s schema and create one if none exists, and then ask if you want to use this web tool or the command-line wizard:\n
         <p>\n        <pre class="border bg-white p-3 m-3"><span style="color:cornflowerblue;">$</span> nf-core launch .\n\n
         ,--./,-.\n          ___     __   __   __   ___     /,-._.--~\\\n    |\\ | |__  __ /  ` /  \\ |__) |__         }  {\n    | \\| |
         \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                          `._,._,\'\n\n    nf-core/tools version 2.3 -
         https://nf-co.re\n\n\n<span style="color:darkblue;">INFO</span>    NOTE:This tool ignores any pipeline parameter defaults overwritten
         by Nextflow config files or profiles\n\n<span style="color:darkblue;">INFO</span>    <span style="color:green;">[&#10003;] Default
         parameters look match schema validation</span>\n<span style="color:darkblue;">INFO</span>    <span style="color:green;">[&#10003;]
         Pipeline schema looks valid</span> (found 72 params)\n\n<span style="color:MediumVioletRed;">Would you like to enter pipeline
         parameters using a web-based interface or a command-line wizard?</span>\n\n<span style="color:darkblue;">?</span> Choose launch method
         (Use arrow keys)\n <span class="text-warning">&#187; Web based</span>\n   Command line</pre>\n\n        <p>If you select <code>Web
         based</code>, then this web page will load with the pipeline parameters for you to fill in.\n            The command-line tool will
         wait for you to click <em>Finished</em> and then offer to run Nextflow with the supplied parameters.</p>\n\n        <p>The command-line
         wizard uses the exact same procedure, but runs entirely locally with a prompt system.\n            That is best for those running on
         offline systems, or if you are concerned about sending sensitive information over the web.</p>\n\n        <p>The nf-core website stores
         a cached copy of your answers for 2 weeks under a random ID.</p>\n\n    '
ERROR    nf-core website API results response not recognised: https://nf-co.re/launch                                                           launch.py:173
          See verbose log for full response

System information

nf-core tools version v2.8 and v2.9 nextflow version 23.04.1.5866

Hardware: Desktop (tested on 3 different workstations) OS ubuntu 20.04

Python 3.9.16

mashehu commented 1 year ago

This is due to a bug after the launch of the new website. For nf-core website, you can in the mean time manually copy-paste the parameter file by going to the website of the pipeline of interest e.g. https://nf-co.re/rnaseq/3.12.0 and hit the launch button on top of that page. Go through all steps and att the end you can copy the parameters from the text field.

We are working on a fix for this issue.

mirpedrol commented 1 year ago

Is this fixed now @mashehu? Can we close the issue?

mashehu commented 1 year ago

yes, should be fixed now