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adding hmmer module & related subworkflows #40

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03f5a3b
adding hmmer module & subworkflows
snafees May 13, 2025
6a964e7
fixed linting
snafees May 13, 2025
e3df838
adding hmmer test & data
snafees May 14, 2025
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14 changes: 14 additions & 0 deletions .nf-test.log
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May-14 01:14:49.220 [main] INFO com.askimed.nf.test.App - nf-test 0.9.2
May-14 01:14:49.227 [main] INFO com.askimed.nf.test.App - Arguments: [test, --verbose, subworkflows/local/hmmer/tests/main.nf.test]
May-14 01:14:49.737 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.04.2
May-14 01:14:49.738 [main] WARN com.askimed.nf.test.commands.RunTestsCommand - No nf-test config file found.
May-14 01:14:49.765 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 33 files from directory /Users/saba.nafees/code/nextflow/proteinannotator in 0.026 sec
May-14 01:14:49.766 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests.
May-14 01:14:49.766 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/Users/saba.nafees/code/nextflow/proteinannotator/subworkflows/local/hmmer/tests/main.nf.test]
May-14 01:14:49.981 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 1 tests to execute.
May-14 01:14:49.982 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan
May-14 01:14:49.982 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Workflow HMMER_ANNOTATION' from file '/Users/saba.nafees/code/nextflow/proteinannotator/subworkflows/local/hmmer/tests/main.nf.test'.
May-14 01:14:49.982 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '67aaf421: Test HMMER database preparation and search'. type: com.askimed.nf.test.lang.workflow.WorkflowTest
May-14 01:14:53.891 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '67aaf421: Test HMMER database preparation and search' finished. status: PASSED
May-14 01:14:53.892 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Workflow HMMER_ANNOTATION' finished. snapshot file: false, skipped tests: false, failed tests: false
May-14 01:14:53.892 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!
95 changes: 95 additions & 0 deletions .nf-test/tests/67aaf421e02387adceb68ea1093eea83/meta/mock.nf
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import groovy.json.JsonGenerator
import groovy.json.JsonGenerator.Converter

nextflow.enable.dsl=2

// comes from nf-test to store json files
params.nf_test_output = ""

// include dependencies


// include test workflow
include { HMMER_ANNOTATION } from '/Users/saba.nafees/code/nextflow/proteinannotator/subworkflows/local/hmmer/tests/../main.nf'

// define custom rules for JSON that will be generated.
def jsonOutput =
new JsonGenerator.Options()
.addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
.build()

def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()

workflow {

// run dependencies


// workflow mapping
def input = []

// Create test protein channel
input[0] = Channel.of(
[
[ id:'test_protein' ],
file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz", checkIfExists: true)
]
)
// Create test HMM database channel (unpressed)
input[1] = Channel.of(
[
[ id:'test_hmm' ],
file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz", checkIfExists: true)
]
)

//----

//run workflow
HMMER_ANNOTATION(*input)

if (HMMER_ANNOTATION.output){

// consumes all named output channels and stores items in a json file
for (def name in HMMER_ANNOTATION.out.getNames()) {
serializeChannel(name, HMMER_ANNOTATION.out.getProperty(name), jsonOutput)
}

// consumes all unnamed output channels and stores items in a json file
def array = HMMER_ANNOTATION.out as Object[]
for (def i = 0; i < array.length ; i++) {
serializeChannel(i, array[i], jsonOutput)
}

}
}


def serializeChannel(name, channel, jsonOutput) {
def _name = name
def list = [ ]
channel.subscribe(
onNext: {
list.add(it)
},
onComplete: {
def map = new HashMap()
map[_name] = list
def filename = "${params.nf_test_output}/output_${_name}.json"
new File(filename).text = jsonOutput.toJson(map)
}
)
}


workflow.onComplete {

def result = [
success: workflow.success,
exitStatus: workflow.exitStatus,
errorMessage: workflow.errorMessage,
errorReport: workflow.errorReport
]
new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)

}
108 changes: 108 additions & 0 deletions .nf-test/tests/67aaf421e02387adceb68ea1093eea83/meta/nextflow.log
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May-14 01:14:50.910 [main] DEBUG nextflow.cli.Launcher - $> nextflow -log /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/meta/nextflow.log run /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test-67aaf421e02387adceb68ea1093eea83.nf -c /Users/saba.nafees/code/nextflow/proteinannotator/nextflow.config -params-file /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/meta/params.json -ansi-log false -with-trace /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/meta/trace.csv -w /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/work
May-14 01:14:50.948 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.2
May-14 01:14:50.960 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/saba.nafees/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2
May-14 01:14:50.966 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
May-14 01:14:50.967 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
May-14 01:14:50.968 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
May-14 01:14:50.974 [main] INFO org.pf4j.AbstractPluginManager - No plugins
May-14 01:14:50.985 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/saba.nafees/code/nextflow/proteinannotator/nextflow.config
May-14 01:14:50.987 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/saba.nafees/code/nextflow/proteinannotator/nextflow.config
May-14 01:14:50.988 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/saba.nafees/code/nextflow/proteinannotator/nextflow.config
May-14 01:14:50.988 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/saba.nafees/code/nextflow/proteinannotator/nextflow.config
May-14 01:14:51.008 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/saba.nafees/.nextflow/secrets/store.json
May-14 01:14:51.010 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@73aff8f1] - activable => nextflow.secret.LocalSecretsProvider@73aff8f1
May-14 01:14:51.021 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
May-14 01:14:51.788 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
May-14 01:14:51.981 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
May-14 01:14:51.988 [main] INFO nextflow.cli.CmdRun - Launching `/Users/saba.nafees/code/nextflow/proteinannotator/.nf-test-67aaf421e02387adceb68ea1093eea83.nf` [confident_hamilton] DSL2 - revision: b9589f0468
May-14 01:14:51.989 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.2.0]
May-14 01:14:51.989 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
May-14 01:14:51.989 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.2.0]
May-14 01:14:51.989 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.2.0
May-14 01:14:51.992 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.2.0' resolved
May-14 01:14:51.993 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.2.0'
May-14 01:14:51.995 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.2.0
May-14 01:14:52.024 [main] DEBUG nextflow.Session - Session UUID: 58ad274a-474b-4ac7-9a94-c1e9bf36c8ad
May-14 01:14:52.024 [main] DEBUG nextflow.Session - Run name: confident_hamilton
May-14 01:14:52.024 [main] DEBUG nextflow.Session - Executor pool size: 14
May-14 01:14:52.027 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
May-14 01:14:52.029 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=42; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-14 01:14:52.040 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.04.2 build 5914
Created: 29-05-2024 06:19 UTC (02:19 EDT)
System: Mac OS X 15.3.1
Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.15+0
Encoding: UTF-8 (UTF-8)
Process: 54157@MacBook-Pro.local [127.0.0.1]
CPUs: 14 - Mem: 96 GB (9.8 GB) - Swap: 0 (0)
May-14 01:14:52.055 [main] DEBUG nextflow.Session - Work-dir: /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/work [Mac OS X]
May-14 01:14:52.055 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/saba.nafees/code/nextflow/proteinannotator/bin
May-14 01:14:52.060 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
May-14 01:14:52.065 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
May-14 01:14:52.078 [main] WARN nextflow.config.Manifest - Invalid config manifest attribute `contributors`
May-14 01:14:52.090 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
May-14 01:14:52.094 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 15; maxThreads: 1000
May-14 01:14:52.123 [main] DEBUG nextflow.Session - Session start
May-14 01:14:52.124 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/meta/trace.csv
May-14 01:14:52.252 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
May-14 01:14:52.569 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-14 01:14:52.570 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-14 01:14:52.572 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
May-14 01:14:52.574 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=14; memory=96 GB; capacity=14; pollInterval=100ms; dumpInterval=5m
May-14 01:14:52.576 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
May-14 01:14:52.605 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-14 01:14:52.606 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-14 01:14:52.611 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name HMMER_ANNOTATION:HMMER_HMMPRESS
May-14 01:14:52.612 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-14 01:14:52.612 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-14 01:14:52.632 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name HMMER_ANNOTATION:HMMER_HMMSEARCH
May-14 01:14:52.634 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-14 01:14:52.634 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-14 01:14:52.653 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
May-14 01:14:52.654 [main] DEBUG nextflow.Session - Igniting dataflow network (7)
May-14 01:14:52.655 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HMMER_ANNOTATION:DECOMPRESS_HMM
May-14 01:14:52.655 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HMMER_ANNOTATION:DECOMPRESS_PROTEINS
May-14 01:14:52.655 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HMMER_ANNOTATION:HMMER_HMMPRESS
May-14 01:14:52.655 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > HMMER_ANNOTATION:HMMER_HMMSEARCH
May-14 01:14:52.655 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_e7e322f88f35de2e: /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test-67aaf421e02387adceb68ea1093eea83.nf
Script_bccdacc34e930bc6: /Users/saba.nafees/code/nextflow/proteinannotator/subworkflows/local/hmmer/tests/../../../../modules/nf-core/hmmer/hmmsearch/main.nf
Script_f4a1ea36ac7c6f03: /Users/saba.nafees/code/nextflow/proteinannotator/subworkflows/local/hmmer/tests/../../../../modules/nf-core/hmmer/hmmpress/main.nf
Script_21a3e529e694b262: /Users/saba.nafees/code/nextflow/proteinannotator/subworkflows/local/hmmer/tests/../main.nf
May-14 01:14:52.655 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
May-14 01:14:52.655 [main] DEBUG nextflow.Session - Session await
May-14 01:14:52.728 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz to work dir: /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/work/stage-58ad274a-474b-4ac7-9a94-c1e9bf36c8ad/7c/ba98106efb21d743695f76bf878eea/e_coli_k12_16s.fna.gz
May-14 01:14:52.728 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz to work dir: /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/work/stage-58ad274a-474b-4ac7-9a94-c1e9bf36c8ad/d9/fc6896eac155200a8ab60b55b99e0e/bac.16S_rRNA.hmm.gz
May-14 01:14:52.846 [Task submitter] WARN n.executor.BashWrapperBuilder - Task runtime metrics are not reported when using macOS without a container engine
May-14 01:14:52.853 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-14 01:14:52.854 [Task submitter] INFO nextflow.Session - [a8/1988a6] Submitted process > HMMER_ANNOTATION:DECOMPRESS_PROTEINS (test_protein)
May-14 01:14:52.859 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-14 01:14:52.860 [Task submitter] INFO nextflow.Session - [0c/cca9d6] Submitted process > HMMER_ANNOTATION:DECOMPRESS_HMM (test_hmm)
May-14 01:14:52.938 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: HMMER_ANNOTATION:DECOMPRESS_PROTEINS (test_protein); status: COMPLETED; exit: 0; error: -; workDir: /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/work/a8/1988a6d2e4f887f2a9328a099f23a7]
May-14 01:14:52.938 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=42; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-14 01:14:52.943 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: HMMER_ANNOTATION:DECOMPRESS_HMM (test_hmm); status: COMPLETED; exit: 0; error: -; workDir: /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/work/0c/cca9d6e3102359210f1879d26ac697]
May-14 01:14:52.963 [TaskFinalizer-2] WARN nextflow.processor.PublishDir - Process `HMMER_ANNOTATION:DECOMPRESS_HMM` publishDir path contains a variable with a null value
May-14 01:14:52.963 [TaskFinalizer-1] WARN nextflow.processor.PublishDir - Process `HMMER_ANNOTATION:DECOMPRESS_PROTEINS` publishDir path contains a variable with a null value
May-14 01:14:52.967 [TaskFinalizer-2] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=42; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-14 01:14:52.969 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-14 01:14:52.969 [Task submitter] INFO nextflow.Session - [12/3df667] Submitted process > HMMER_ANNOTATION:HMMER_HMMPRESS (test_hmm)
May-14 01:14:52.973 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-14 01:14:52.973 [Task submitter] INFO nextflow.Session - [73/044ac4] Submitted process > HMMER_ANNOTATION:HMMER_HMMSEARCH (test_protein)
May-14 01:14:53.092 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: HMMER_ANNOTATION:HMMER_HMMPRESS (test_hmm); status: COMPLETED; exit: 0; error: -; workDir: /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/work/12/3df6677fcee297119e730c26d2869d]
May-14 01:14:53.095 [TaskFinalizer-3] WARN nextflow.processor.PublishDir - Process `HMMER_ANNOTATION:HMMER_HMMPRESS` publishDir path contains a variable with a null value
May-14 01:14:53.159 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: HMMER_ANNOTATION:HMMER_HMMSEARCH (test_protein); status: COMPLETED; exit: 0; error: -; workDir: /Users/saba.nafees/code/nextflow/proteinannotator/.nf-test/tests/67aaf421e02387adceb68ea1093eea83/work/73/044ac4d02da6ece722d5d629a93952]
May-14 01:14:53.163 [TaskFinalizer-4] WARN nextflow.processor.PublishDir - Process `HMMER_ANNOTATION:HMMER_HMMSEARCH` publishDir path contains a variable with a null value
May-14 01:14:53.165 [main] DEBUG nextflow.Session - Session await > all processes finished
May-14 01:14:53.264 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
May-14 01:14:53.264 [main] DEBUG nextflow.Session - Session await > all barriers passed
May-14 01:14:53.266 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
May-14 01:14:53.266 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
May-14 01:14:53.275 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=4; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=696ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=7; peakMemory=42 GB; ]
May-14 01:14:53.275 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
May-14 01:14:53.275 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
May-14 01:14:53.774 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
May-14 01:14:53.844 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
May-14 01:14:53.852 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-schema@2.2.0'
May-14 01:14:53.852 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-schema
May-14 01:14:53.852 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
May-14 01:14:53.852 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
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