Adding the Installer for mac

INSTALL_MAC.sh

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+#!/bin/zsh
+brew install openjdk@17 
+echo 'export PATH="/opt/homebrew/opt/openjdk@17/bin:$PATH"' >> ~/.zshrc  
+source ~/.zshrc 
+java -version
+
+# Install Nextflow
+export CAPSULE_LOG=none
+curl -s https://get.nextflow.io | bash
+sudo mv nextflow /usr/local/bin/
+chmod +x /usr/local/bin/nextflow
+
+# Check info
+nextflow -version
+nextflow info   

LEARN.md

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+# Nextflow Command Reference
+
+This is a tutorial  [link][ref].
+
+ [ref]: https://training.nextflow.io/latest/  "Tutorial"
+
+This is a container reg (seqera)  [link][ref].
+
+ [ref]: https://seqera.io/containers/ "Container"
+
+Searched container example (MAC arm) [link][ref].
+
+[ref]: https://seqera.io/containers/?packages=conda-forge::cowpy=1.1.5 "Container Search cowpy"
+
+## Check the Nextflow Version
+```sh
+nextflow -v
+```
+
+# Run a Nextflow Pipeline 
+```sh
+nextflow run <File.nf>
+```
+# Resume a Previous Run
+```sh
+nextflow run hello-world.nf -resume
+```
+# View Nextflow Logs
+```sh
+nextflow log 
+```
+
+# Dry Run (Preview):
+```sh
+nextflow clean -before <runnamefromlog> -n
+```
+-n is for a dry run (shows what would be deleted).
+
+Force Clean (Delete):
+```sh
+nextflow clean -before <runnamefromlog> -f
+```
+-f is for force (actually deletes files).
+
+# Passing a variabe 
+```sh
+nextflow run hello-world.nf --greeting "Hek varlden"
+```
+---
+# More options 
+Trace Report
+Creates a tabular text file with detailed info about every process:
+```sh 
+nextflow run pipeline.nf -with-trace
+```
+
+Execution Report (HTML)
+Generates a report.html file with pipeline stats.
+```sh
+nextflow run pipeline.nf -with-report
+```
+Timeline Visualization (HTML)
+Generates a timeline.html showing process flow and duration.
+```sh
+nextflow run pipeline.nf -with-timeline
+```
+Execution DAG
+Creates a flow chart of your pipeline.
+```sh
+nextflow run pipeline.nf -with-dag flowchart.png
+```
+Input variables 
+Calling an input varibale with the value, we can also use the default value
+```sh
+nextflow run hello-world.nf --greeting "He Ali" -with-report  
+nextflow run hello-world.nf
+```
+Output 
+```
+nextflow run hello-channels.nf -ansi-log false 
+```
+Operators
+```
+ #useed for array, ref ex 03
+ .flatten()
+
+ #Used to read file csv, ref ex 03
+ .splitCsv()
+
+ # view before and after, ref ex 03
+ .view()
+
+ # Concatinate all the output to single file, ref ex 04
+ .collect() 
+
+ # Count the size of the input channel and assign it to the variable 
+.size()
+```
+Workflow 
+```
+Pipeline run in parallel, till now we only check the single process workflow
+1. How we will use channels to connect those steps 
+2. Multiple tasks, which can collapse into a single process 
+3. We also look the process with multiple inputs and multiple outputs 
+```
+MultiInput, ref ex 05
+```
+# overriding the default value from input variable 
+nextflow run hello-workflow.nf --batch_name "demo-output"
+
+```
+Multiple Output, ref ex 06 
+```
+# Using the emit to access them in positional manner, like a decorator
+```
+Nextflow Module Ex 07 
+```
+Example NF Core Module repository 
+include { sayHello } from './modules/sayHello.nf'
+
+```
+Container 
+```
+Community run container 
+
+Run the singularity 
+
+# Pull the singularity image 
+apptainer pull cowpy.sif https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bde91ba24078478208035944326ee69a6063ae0f29523e017840e863c42e0b93/data
+
+Run the docker
+
+# Pull the image from seqera 
+docker pull community.wave.seqera.io/library/cowpy:1.1.5--1a5414f41afdfd25
+
+# run the image
+docker run --rm community.wave.seqera.io/library/cowpy:1.1.5--1a5414f41afdfd25  cowpy
+
+docker run -it community.wave.seqera.io/library/cowpy:1.1.5--1a5414f41afdfd25  /bin/bash
+
+# mount a directory 
+docker run --rm -it -v .:/data community.wave.seqera.io/library/cowpy:1.1.5--1a5414f41afdfd25  /bin/bash
+
+# run this CLI inside the container 
+cowpy "Hello Containers" -c tux
+cowpy "Hello Containers" -c cheese 
+cowpy "Hello Containers" -c dragonandcow
+Run the podman
+```

my_pipeline/01-hello-nextflow/hello-world.nf

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+#!/usr/bin/env nextflow
+
+/*
+ * Use echo to print 'Hello World!' to a file
+ */
+process sayHello {
+
+    publishDir 'results', mode: 'copy'
+
+    input:
+    val greeting
+
+    output:
+        path 'output.txt'
+
+    script:
+    """
+    echo '$greeting' > output.txt
+    """
+}
+
+/* * Passing default parameters to the workflow */
+params.greeting = 'Hello World!'
+
+workflow {
+
+    // emit a greeting
+    sayHello(params.greeting)
+}

my_pipeline/01-hello-nextflow/trace-20250703-60404614.txt

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+task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
+1	d8/229586	86298	sayHello	COMPLETED	0	2025-07-03 16:46:45.274	62ms	0ms	-	-	-	-	-

my_pipeline/02-hello-channel/hello-channels.nf

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+#!/usr/bin/env nextflow
+
+/*
+ * Use echo to print 'Hello World!' to a file
+ */
+process sayHello {
+
+    publishDir 'results', mode: 'copy'
+
+    input:
+    val greeting
+
+    output:
+        path "$greeting-output.txt"
+
+    script:
+    """
+    echo '$greeting' > '$greeting-output.txt'
+    """
+}
+
+/* * Passing default parameters to the workflow */
+params.greeting = 'Hello World!'
+
+workflow {
+    greetings_array = [params.greeting, 'Hello, Nextflow!', 'Greetings, NF!']
+    greeting_ch = channel.of(greetings_array)
+                         .view{ greeting -> "Before flatten: $greeting" }
+                         .flatten()
+                         .view{ greeting -> "After flatten: $greeting" }
+
+    // emit a greeting
+    // nf created the channels automatically
+    sayHello(greeting_ch)
+}

my_pipeline/03-hello-channel-file-input/greetings.csv

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+Hello
+Bonjour
+Hola

my_pipeline/03-hello-channel-file-input/hello-channels.nf

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+#!/usr/bin/env nextflow
+
+/*
+ * Use echo to print 'Hello World!' to a file
+ */
+process sayHello {
+
+    publishDir 'results', mode: 'copy'
+
+    input:
+    val greeting
+
+    output:
+        path "$greeting-output.txt"
+
+    script:
+    """
+    echo '$greeting' > '$greeting-output.txt'
+    """
+}
+
+/* * Passing default parameters to the workflow */
+params.greeting = 'greetings.csv'
+
+workflow {
+    // create a channel from the CSV file
+    greeting_ch = channel.fromPath(params.greeting)
+                         .view{ csv -> "Before splitCsv: $csv" }
+                         .splitCsv()
+                         .view{ csv -> "After splitCsv: $csv" }
+                         .map{ item -> item[0] }
+                         .view{ csv -> "After map: $csv" }
+
+    // emit a greeting
+    // nf created the channels automatically
+    sayHello(greeting_ch)
+}

my_pipeline/04-hello-workflow/greetings.csv

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+Hello
+Bonjour
+Hola

my_pipeline/04-hello-workflow/hello-workflow.nf

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+#!/usr/bin/env nextflow
+
+/*
+ * Use echo to print 'Hello World!' to a file
+ */
+process sayHello {
+
+    publishDir 'results', mode: 'copy'
+
+    input:
+    val greeting
+
+    output:
+        path "$greeting-output.txt"
+
+    script:
+    """
+    echo '$greeting' > '$greeting-output.txt'
+    """
+}
+
+process convertToUppercase {
+
+    publishDir 'results', mode: 'copy'
+
+    input:
+    path input_file
+
+    output:
+        path "UPPER-${input_file}-output.txt"
+
+    script:
+    """
+    cat $input_file | tr '[a-z]' '[A-Z]' > "UPPER-${input_file}-output.txt"
+    """
+}
+
+process collectGreetings {
+
+    publishDir 'results', mode: 'copy'
+
+    input:
+    path input_file
+
+    output:
+        path "COLLECTED-output.txt"
+
+    script:
+    """
+    cat $input_file > "COLLECTED-output.txt"
+    """
+}
+
+/* * Passing default parameters to the workflow */
+params.greeting = 'greetings.csv'
+
+workflow {
+    // create a channel from the CSV file
+    greeting_ch = channel.fromPath(params.greeting)
+                         .view{ csv -> "Before splitCsv: $csv" }
+                         .splitCsv()
+                         .view{ csv -> "After splitCsv: $csv" }
+                         .map{ item -> item[0] }
+                         .view{ csv -> "After map: $csv" }
+
+    // emit a greeting
+    // nf created the channels automatically
+    sayHello(greeting_ch)
+
+    // Convert the output of sayHello to uppercase
+    convertToUppercase(sayHello.out)
+
+    // Collect all greetings into a single file
+    collectGreetings(sayHello.out.collect())
+    convertToUppercase.out.view{ greetings -> "Before collectGreetings: $greetings" }
+    convertToUppercase.out.collect()
+        .view{ greetings -> "After collectGreetings: $greetings" }
+
+
+}

my_pipeline/05-hello-workflow-multi-input/greetings.csv

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+Hello
+Bonjour
+Hola