diff --git a/README.md b/README.md
index 5219af899716c193a2d76ea7b99f23939feb2cbc..a738049fe527f4bff967d22a3042ed5ade0558a3 100755
--- a/README.md
+++ b/README.md
@@ -97,7 +97,7 @@ The default values for all parameters are set in `src/nexflow.config`. Please no
 ```txt
 --step
 
-<Type: String. Options are "1", "2_from_step_1", "2_from_minknow", "3". Select 1 for basecalling. Select "2_from_step_1" for alignment filtering and quality control continuing after executing step 1 of this pipeline. Select "2_from_minknow" for alignment filtering and quality control from input basecalled using MinKNOW. Select "3" for methylation call pre-processing with modkit and generating a thorough multiQC report for sequencing stats. This parameter needs to be set for the pipeline to run. Default: "None">
+<Type: String. Options are "all", "1", "2_from_step_1", "2_from_minknow", "3". Select "all" to execute steps "1", "2_from_step_1" and "3". Select "1" for basecalling. Select "2_from_step_1" for alignment filtering and quality control continuing after executing step 1 of this pipeline. Select "2_from_minknow" for alignment filtering and quality control from input basecalled using MinKNOW. Select "3" for methylation call pre-processing with modkit and generating a thorough multiQC report for sequencing stats. This parameter needs to be set for the pipeline to run. Default: "None">
 ```
 
 ```txt
diff --git a/src/configs/human_blood.config b/src/configs/human_blood.config
index 9560781f2cb418e78d301b1b3a81a953a9ba5d24..0f3b8688b8cb3956aaf0c8cadd9ef4d8db1b7dcc 100644
--- a/src/configs/human_blood.config
+++ b/src/configs/human_blood.config
@@ -25,4 +25,14 @@ profiles {
             out_dir = "results_human_blood/"
         }
     }
-}
\ No newline at end of file
+    human_blood {
+        params {
+            project_name = "results_human_blood"
+            step = "all"
+            basecall_path = "./data/pod5"
+            reference_file = "./references/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
+            steps_2_and_3_input_directory = "./results/results_human_blood/"
+            out_dir = "results_human_blood/"
+        }
+    }
+}
diff --git a/src/main.nf b/src/main.nf
index d38bd5e9a79f76d9d661ec903de132c9c37a42e1..e79677911038eb909c587dc3163e81db46a77346 100755
--- a/src/main.nf
+++ b/src/main.nf
@@ -6,8 +6,10 @@ include {MODKIT_AND_MULTIQC} from './sub_workflows/MODKIT_AND_MULTIQC.nf'
 
 // Main workflow logic
 workflow {
-    // Log execution parameters
-    if (params.step.toString() == "1") {
+    valid = false
+    if (params.step.toString() == "all" || params.step.toString() == "1") {
+        valid = true
+        // Log execution parameters
         log.info """
         =================================================================
         STEP 1 - OXFORD NANOPORE DNA SEQUENCING BASECALLING AND ALIGNMENT
@@ -24,34 +26,8 @@ workflow {
         GPU device for submission                           : ${params.gpu_devices}
         Output directory                                    : ${params.out_dir}
         =================================================================
-        """ 
-    } else if (params.step.toString() == "2_from_step_1" || params.step.toString() == "2_from_minknow") {
-        log.info """
-        ======================================
-        STEP 2 - FILTERING AND QUALITY CONTROL
-        ======================================
-        Input directory (output dir from step 1)            : ${params.steps_2_and_3_input_directory}
-        Basecall quality score threshold                    : ${params.qscore_thresh}
-        MAPQ filtering threshold							: ${params.mapq}
-        Min number of mapped reads per sample/barcode       : ${params.min_mapped_reads_thresh}
-        BAM files barcoded?                 				: ${params.is_barcoded}
-        ======================================
         """
-    } else if (params.step.toString() == "3") {
-        log.info """
-        ===============================================
-        STEP 3 - METHYLATION CALLING AND MULTIQC REPORT
-        ===============================================
-        Input directory (input dir from step 2)             : ${params.steps_2_and_3_input_directory}
-        MultiQC configuration file                          : ${params.multiqc_config}
-        ===============================================
-        """
-    } else {
-        println "ERROR: You must set parameter --step to '1' or '2_from_step_1' or '2_from_minknow' or '3'. Please refer to documentation at: https://gmapsrv.pucrs.br/gitlab/ccd-public/nanopore"
-        System.exit(1)
-    }
-    // Set initial files and channels
-    if (params.step.toString() == "1") {
+        // Set initial files and channels
         if (params.prefix == "None") {
             fast5_path = Channel.fromPath("${params.basecall_path}/**.fast5").map{file -> tuple(file.parent.toString().split("/")[-3] + "_" + file.simpleName.split('_')[0] + "_" + file.simpleName.split('_')[-3..-2].join("_"), file) }.groupTuple()
             pod5_path = Channel.fromPath("${params.basecall_path}/**.pod5").map{file -> tuple(file.parent.toString().split("/")[-3] + "_" + file.simpleName.split('_')[0] + "_" + file.simpleName.split('_')[-3..-2].join("_"), file) }.groupTuple()
@@ -68,16 +44,52 @@ workflow {
         trimmed_barcodes = Channel.value(params.trimmed_barcodes)
         gpu_devices = Channel.value(params.gpu_devices)
         reference_file = file(params.reference_file)
-    } else if (params.step.toString() == "2_from_step_1") {
-        bam_files = Channel.fromPath("${params.steps_2_and_3_input_directory}/basecalling_output/*.bam").map {file -> tuple(file.baseName, file) }.toSortedList( { a, b -> a[0] <=> b[0] } ).flatten().buffer(size:2) 
-        txt_files = Channel.fromPath("${params.steps_2_and_3_input_directory}/basecalling_output/*.txt").toSortedList( { a, b -> a.baseName <=> b.baseName } ).flatten()
-        mapq = Channel.value(params.mapq)
-        qscore_thresh = Channel.value(params.qscore_thresh)
-    } else if (params.step.toString() == "2_from_minknow") {
-        input_dir = Channel.fromPath("${params.steps_2_and_3_input_directory}/")
-        mapq = Channel.value(params.mapq)
-        qscore_thresh = Channel.value(params.qscore_thresh)
-    } else if (params.step.toString() == "3") {
+        // Run steps
+        BASECALLING(pod5_path, fast5_path, basecall_speed, basecall_mods, basecall_config, basecall_trim, qscore_thresh, barcoding_kit, trimmed_barcodes, gpu_devices, reference_file)
+    }
+    if (params.step.toString() == "all" || params.step.toString() == "2_from_step_1" || params.step.toString() == "2_from_minknow") {
+        valid = true
+        // Log execution parameters
+        log.info """
+        ======================================
+        STEP 2 - FILTERING AND QUALITY CONTROL
+        ======================================
+        Input directory (output dir from step 1)            : ${params.steps_2_and_3_input_directory}
+        Basecall quality score threshold                    : ${params.qscore_thresh}
+        MAPQ filtering threshold                            : ${params.mapq}
+        Min number of mapped reads per sample/barcode       : ${params.min_mapped_reads_thresh}
+        BAM files barcoded?                                 : ${params.is_barcoded}
+        ======================================
+        """
+        if (params.step.toString() == "all" || params.step.toString() == "2_from_step_1") {
+            // Set initial files and channels
+            bam_files = Channel.fromPath("${params.steps_2_and_3_input_directory}/basecalling_output/*.bam").map {file -> tuple(file.baseName, file) }.toSortedList( { a, b -> a[0] <=> b[0] } ).flatten().buffer(size:2) 
+            txt_files = Channel.fromPath("${params.steps_2_and_3_input_directory}/basecalling_output/*.txt").toSortedList( { a, b -> a.baseName <=> b.baseName } ).flatten()
+            mapq = Channel.value(params.mapq)
+            qscore_thresh = Channel.value(params.qscore_thresh)
+            // Run steps
+            FILTERING_AND_QC_FROM_STEP_1(bam_files, txt_files, mapq, qscore_thresh)
+        } else if (params.step.toString() == "2_from_minknow") {
+            // Set initial files and channels
+            input_dir = Channel.fromPath("${params.steps_2_and_3_input_directory}/")
+            mapq = Channel.value(params.mapq)
+            qscore_thresh = Channel.value(params.qscore_thresh)
+            // Run steps
+            FILTERING_AND_QC_FROM_MINKNOW(input_dir, mapq, qscore_thresh)
+        }
+    }
+    if (params.step.toString() == "all" || params.step.toString() == "3") {
+        valid = true
+        // Log execution parameters
+        log.info """
+        ===============================================
+        STEP 3 - METHYLATION CALLING AND MULTIQC REPORT
+        ===============================================
+        Input directory (input dir from step 2)             : ${params.steps_2_and_3_input_directory}
+        MultiQC configuration file                          : ${params.multiqc_config}
+        ===============================================
+        """
+        // Set initial files and channels
         filtered_bams = Channel.fromPath("${params.steps_2_and_3_input_directory}/bam_filtering/*-Filtered*.bam").map {file -> tuple(file.baseName, file) }.toSortedList( { a, b -> a[0] <=> b[0] } ).flatten().buffer(size:2) 
         filtered_bais = Channel.fromPath("${params.steps_2_and_3_input_directory}/bam_filtering/*-Filtered*.bam.bai").toSortedList( { a, b -> a.baseName <=> b.baseName } ).flatten() 
         num_reads = Channel.fromPath("${params.steps_2_and_3_input_directory}/intermediate_qc_reports/number_of_reads/*")
@@ -85,15 +97,12 @@ workflow {
         quality_thresholds = Channel.fromPath("${params.steps_2_and_3_input_directory}/intermediate_qc_reports/quality_score_thresholds/*")
         multiqc_config = Channel.fromPath(params.multiqc_config)
         multiqc_input = Channel.fromPath("${params.steps_2_and_3_input_directory}/multiqc_input/**", type: "file")
-    }
-    // Run steps
-    if (params.step.toString() == "1") {
-        BASECALLING(pod5_path, fast5_path, basecall_speed, basecall_mods, basecall_config, basecall_trim, qscore_thresh, barcoding_kit, trimmed_barcodes, gpu_devices, reference_file)
-    } else if (params.step.toString() == "2_from_step_1") {
-        FILTERING_AND_QC_FROM_STEP_1(bam_files, txt_files, mapq, qscore_thresh)
-    } else if (params.step.toString() == "2_from_minknow") {
-        FILTERING_AND_QC_FROM_MINKNOW(input_dir, mapq, qscore_thresh)
-    } else if (params.step.toString()== "3") {
+        // Run steps
         MODKIT_AND_MULTIQC(filtered_bams, filtered_bais, num_reads, read_length, quality_thresholds, multiqc_config, multiqc_input)
     }
+    if (!valid) {
+        // Log execution parameters
+        println "ERROR: You must set parameter --step to 'all', '1' or '2_from_step_1' or '2_from_minknow' or '3'. Please refer to documentation at: https://gmapsrv.pucrs.br/gitlab/ccd-public/nanopore"
+        System.exit(1)
+    }
 }